Start menu duplicate Shortcuts
This answer is for Windows build 15063 (Creator Update)
If Charlie C's answer doesn't work (in my case It's even get worse, having triplicate to three tiles per shortcut), please try this:
Go to the start menu shortcut folder (e.g. C:\Users\\AppData\Roaming\Microsoft\Windows\Start Menu\Programs). Locate the problematic shortcut, made a copy of it to the same folder.
Unpin the last problematic tile in the start menu. You will notice that instead of the latest one, the first duplicate disappear instead.
Go back to the start menu folder, delete the original problematic shortcut. (keep the copy).
Back to start menu, the remaining problematic tiles will change their name to the name of the copy of the shortcut (something like - Copy).
Now you have one less duplicate tiles. Repeat step 1-4 until a single tile of the shortcut left.
Your TileDataLayer has been corrupted or damaged.
Run the following command to see if it helps.
Open Powershell as an Administrator. This will reset your TileDataLayer cache, re-register applications in the start menu, and reset the layout.
Give it about 10 minutes to complete, and reboot the machine.
TDLrecover.exe -resetcache -resetlayout -reregister -allowparallel
If this does not resolve your issue, your profile is corrupt and needs to be recreated.