Bootstrap 4 content and navigation side bar Overlap issue

change your .sidenav{position:fixed; top:0;} to .sidenav{position:absolute; top:5%;}

function openNav() {
    document.getElementById("mySidenav").style.width = "250px";
  }

  function closeNav() {
    document.getElementById("mySidenav").style.width = "0";
  }
body.mainbody {
  overflow: hidden;

  font: 13px/1.7em 'sans-serif';
  font-family: sans-serif;
}

html, body {
  height: 100%;
  width: 100%;
  margin: 0;
  padding: 0;
}

.bg-inverse {
  background-color: grey !important;
}

.header {
  width: 100%;
  height: 5%;

  background: red;
  position: fixed;
  top: 0;
}

.footer {
  width: 100%;
  height: 60px;
  background: grey;
  position: fixed;
  bottom: 0;

}

.main-content{
  height: 85%;
  margin-top:11%;
z-index: 0; overflow-y: scroll;
}

#content-top {
  width: 100%;
  top: 5%;
  height: 5%;
  padding: 1.5%;z-index: -1;
background-color: white;
  position: fixed;
}
#content-top-fat {
  width: 100%;
  top: 5%;
  background-color: white;
  height: 5%;
  padding: 1.5%;
  z-index: 1;
  position: fixed;
}
#content-bot-fat {
  width: 100%;
  top: 10%;  z-index: -1;
  height: 5%;
  padding: 1.5%;
  background:white;
  position: fixed;
}
.p-2 {
  padding: 0.4em 0.5rem !important;
}
#contents {
  /*position: fixed;*/

  overflow-x: hidden;
margin-top: 5.0rem;
padding: 2%;
}


.sidenav {
  height: 100%;
  width: 0;
  position: absolute;
  z-index: 5;
  top: 5%;
  right: 0;
  background-color: #eee;
  overflow-x: hidden;
  transition: 0.5s;
  padding-top: 60px;
}

.sidenav a {
  padding: 8px 8px 8px 32px;
  text-decoration: none;
  font-size: 25px;
  color: #818181;
  display: block;
  transition: 0.3s;
}

.sidenav a:hover, .offcanvas a:focus{
  color: #f1f1f1;
}

.sidenav .closebtn {
  position: absolute;
  top: 0;
  right: 25px;
  font-size: 36px;
  margin-left: 50px;
}

@media screen and (max-height: 450px) {
  .sidenav {padding-top: 15px;}
  .sidenav a {font-size: 18px;}
}
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.6/css/bootstrap.min.css" rel="stylesheet"/>
<body class="mainbody">
<div class="header">
<div class="d-flex justify-content-end">
  <div class="mr-auto p-2">Dashboard</div>
  <div class="p-2"></div>
  <div class="p-2"><span style="font-size:30px;cursor:pointer" onclick="openNav()">&#9776; </span></div>
</div>


</div>
<div id="mySidenav" class="sidenav">
  <a href="javascript:void(0)" class="closebtn" onclick="closeNav()">&times;</a>
  <a href="#">About</a>
  <a href="#">Services</a>
  <a href="#">Clients</a>
  <a href="#">Contact</a>
</div>
<!--/header-->
<div id="content-top-fat">
  <div class="add-text-fat">
    <div class="d-inline-flex ">+</div>
    <div class="d-inline-flex ">Add New Rate Plan</div>

  </div>


</div>
<div id="content-bot-fat">


  <div class="d-flex justify-content-center"><p class="rateplan-date">Thursday, April, 20, 2017
  </p></div>
</div>
<!--content-->
<div class="main-content">
  <div id="contents">
 

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.




Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with p
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

Components
Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.
  </div>
</div>

<div class="footer"></div>
</body>

Looks like it's just a z-index issue that can be resolved by moving z-index: 5 from .sidenav to .header

function openNav() {
    document.getElementById("mySidenav").style.width = "250px";
  }

  function closeNav() {
    document.getElementById("mySidenav").style.width = "0";
  }
body.mainbody {
  overflow: hidden;
  font: 13px/1.7em 'sans-serif';
  font-family: sans-serif;
}

html, body {
  height: 100%;
  width: 100%;
  margin: 0;
  padding: 0;
}

.bg-inverse {
  background-color: grey !important;
}

.header {
  width: 100%;
  height: 5%;
  z-index: 5;
  background: red;
  position: fixed;
  top: 0;
}

.footer {
  width: 100%;
  height: 60px;
  background: grey;
  position: fixed;
  bottom: 0;

}

.main-content{
  height: 85%;
  margin-top:5%;
z-index: -1; overflow-y: scroll;
}

#content-top {
  width: 100%;
  top: 5%;
  height: 5%;
  padding: 1.5%;z-index: -1;
background-color: white;
  position: fixed;
}
#content-top-fat {
  width: 100%;
  top: 5%;
  background-color: white;
  height: 5%;
  padding: 1.5%;
  z-index: 1;
  position: fixed;
}
#content-bot-fat {
  width: 100%;
  top: 10%;  z-index: -1;
  height: 5%;
  padding: 1.5%;
  background:white;
  position: fixed;
}
.p-2 {
  padding: 0.4em 0.5rem !important;
}
#contents {
  /*position: fixed;*/

  overflow-x: hidden;
margin-top: 6.5rem;
padding: 2%;
}


.sidenav {
  height: 100%;
  width: 0;
  position: fixed;
  top: 0;
  right: 0;
  background-color: #eee;
  overflow-x: hidden;
  transition: 0.5s;
  padding-top: 60px;
}

.sidenav a {
  padding: 8px 8px 8px 32px;
  text-decoration: none;
  font-size: 25px;
  color: #818181;
  display: block;
  transition: 0.3s;
}

.sidenav a:hover, .offcanvas a:focus{
  color: #f1f1f1;
}

.sidenav .closebtn {
  position: absolute;
  top: 0;
  right: 25px;
  font-size: 36px;
  margin-left: 50px;
}

@media screen and (max-height: 450px) {
  .sidenav {padding-top: 15px;}
  .sidenav a {font-size: 18px;}
}
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.6/css/bootstrap.min.css" rel="stylesheet"/>
<body class="mainbody">
<div class="header">
<div class="d-flex justify-content-end">
  <div class="mr-auto p-2">Dashboard</div>
  <div class="p-2"></div>
  <div class="p-2"><span style="font-size:30px;cursor:pointer" onclick="openNav()">&#9776; </span></div>
</div>

<div id="mySidenav" class="sidenav">
  <a href="javascript:void(0)" class="closebtn" onclick="closeNav()">&times;</a>
  <a href="#">About</a>
  <a href="#">Services</a>
  <a href="#">Clients</a>
  <a href="#">Contact</a>
</div>
</div>
<!--/header-->
<div id="content-top-fat">
  <div class="add-text-fat">
    <div class="d-inline-flex ">+</div>
    <div class="d-inline-flex ">Add New Rate Plan</div>

  </div>


</div>
<div id="content-bot-fat">


  <div class="d-flex justify-content-center"><p class="rateplan-date">Thursday, April, 20, 2017
  </p></div>
</div>
<!--content-->
<div class="main-content">
  <div id="contents">
 

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.




Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with p
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

Components
Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.
  </div>
</div>

<div class="footer"></div>
</body>

I have found the problem in your code and I have fixed it. I hope it will help you :)

function openNav() {
    document.getElementById("mySidenav").style.width = "250px";
  }

  function closeNav() {
    document.getElementById("mySidenav").style.width = "0";
  }
body.mainbody {
  overflow: hidden;

  font: 13px/1.7em 'sans-serif';
  font-family: sans-serif;
}

html, body {
  height: 100%;
  width: 100%;
  margin: 0;
  padding: 0;
}

.bg-inverse {
  background-color: grey !important;
}

.header {
  width: 100%;
  height: 5%;

  background: red;
  position: fixed;
  top: 0;
}

.footer {
  width: 100%;
  height: 60px;
  background: grey;
  position: fixed;
  bottom: 0;

}

.main-content{
  height: 85%;
  margin-top:11%;
z-index: 0; overflow-y: scroll;
}

#content-top {
  width: 100%;
  top: 5%;
  height: 5%;
  padding: 1.5%;z-index: -1;
background-color: white;
  position: fixed;
}
#content-top-fat {
  width: 100%;
  top: 5%;
  background-color: white;
  height: 5%;
  padding: 1.5%;
  z-index: 1;
  position: fixed;
}
#content-bot-fat {
  width: 100%;
  top: 10%;  z-index: -1;
  height: 5%;
  padding: 1.5%;
  background:white;
  position: fixed;
}
.p-2 {
  padding: 0.4em 0.5rem !important;
}
#contents {
  /*position: fixed;*/

  overflow-x: hidden;
margin-top: 5.0rem;
padding: 2%;
}


.sidenav {
  height: 100%;
  width: 0;
  position: absolute;
  z-index: 5;
  top: 5%;
  right: 0;
  background-color: #eee;
  overflow-x: hidden;
  transition: 0.5s;
  padding-top: 60px;
}

.sidenav a {
  padding: 8px 8px 8px 32px;
  text-decoration: none;
  font-size: 25px;
  color: #818181;
  display: block;
  transition: 0.3s;
}

.sidenav a:hover, .offcanvas a:focus{
  color: #f1f1f1;
}

.sidenav .closebtn {
  position: absolute;
  top: 0;
  right: 25px;
  font-size: 36px;
  margin-left: 50px;
}

@media screen and (max-height: 450px) {
  .sidenav {padding-top: 15px;}
  .sidenav a {font-size: 18px;}
}
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.6/css/bootstrap.min.css" rel="stylesheet"/>
<body class="mainbody">
<div class="header">
<div class="d-flex justify-content-end">
  <div class="mr-auto p-2">Dashboard</div>
  <div class="p-2"></div>
  <div class="p-2"><span style="font-size:30px;cursor:pointer" onclick="openNav()">&#9776; </span></div>
</div>


</div>
<div id="mySidenav" class="sidenav">
  <a href="javascript:void(0)" class="closebtn" onclick="closeNav()">&times;</a>
  <a href="#">About</a>
  <a href="#">Services</a>
  <a href="#">Clients</a>
  <a href="#">Contact</a>
</div>
<!--/header-->
<div id="content-top-fat">
  <div class="add-text-fat">
    <div class="d-inline-flex ">+</div>
    <div class="d-inline-flex ">Add New Rate Plan</div>

  </div>


</div>
<div id="content-bot-fat">


  <div class="d-flex justify-content-center"><p class="rateplan-date">Thursday, April, 20, 2017
  </p></div>
</div>
<!--content-->
<div class="main-content">
  <div id="contents">
 

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.




Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with p
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.Preprocessor
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.
Bootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

ComponentsBootstrap ships with vanilla CSS, but its source code utilizes Sass, a popular CSS preprocessor. Quickly get started with precompiled CSS or build on the source.

Responsive across devices
One framework, every device.
Bootstrap easily and efficiently scales your websites and applications with a single code base, from phones to tablets to desktops with CSS media queries.

Components
Components
Full of features
With Bootstrap, you get extensive and beautiful documentation for common HTML elements, dozens of custom HTML and CSS components, and awesome jQuery plugins.
  </div>
</div>

<div class="footer"></div>
</body>