pdfTeX warning (ext4): destination with the same identifier (nam e{page.1}) has been already used, duplicate ignored

One way to avoid the problem is to change the (invisible) numbering style of the title page:

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[pdfpagelabels]{hyperref}

\title{[Title]}
\author{N.N.}

\begin{document}

\pagenumbering{Alph}
\begin{titlepage}
\maketitle
\thispagestyle{empty}
\end{titlepage}
\pagenumbering{arabic}

\tableofcontents
\thispagestyle{empty}

\newpage

\section{[Section]}

\end{document}

As requested by the comments: Another way to solve it is to disable the pageanchors for the titlepage:

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[pdfpagelabels]{hyperref}

\title{[Title]}
\author{N.N.}

\begin{document}

\hypersetup{pageanchor=false}
\begin{titlepage}
\maketitle
\end{titlepage}

\hypersetup{pageanchor=true}
\pagenumbering{arabic}
\tableofcontents

\section{[Section]}
\end{document}

It is a matter of taste which solution is better. hyperref needs page anchors with unique names e.g. to add links to the index. Changing the page numbering style as Enrico did in his answer is a logical and adequate method to do it. On the other side: If there is a part of the document where one don't need pageanchors, disabling them is also adequate.

I am required to use a template from my university, hence, there is no freedom to move parts of the document into different places. My understanding is that many packages conflict with hyperref (See https://texfaq.org/FAQ-hyperdupdest), the only thing that worked for me was to load the float package before hyperref.

\usepackage{float}
\usepackage{hyperref}