This problem was there in Ubuntu (GNOME) 16.04, and still remains in
16.10. It seems that the duplicate entries come from multiple .desktop
files in /usr/share/applications/. There is also a duplicate entry for
Rhythmbox that appears in "Open with..." prompts, etc. (One of the
Rhythmbox entries is for selecting an input source, but the name in the
.desktop file is the same as the one for the main entry.) All this may
be because of providing entries for the Ubuntu Unity desktop.

Deleting or renaming one .desktop file for File Roller does remove the
duplicate entry for Archive Manager while having no ill-effects, but
deleting or renaming one or other of the .desktop files for Nautilus
causes the Files entry to disappear from either the dash or the
Applications menu. In any case, an update to any of the applications
will put the .desktop file and thus the duplicate entry back again, and
it will be a matter of constantly correcting /usr/share/applications/
manually or automatically; a less than desirable workaround. Comparing
with another standard GNOME desktop, such as in Fedora Workstation, and
investigating possible conflicts with entries meant for the Unity
desktop may help. One option may be to tweak the "OnlyShowIn" entries in
the .desktop files.

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https://bugs.launchpad.net/bugs/1562409

Title:
  notifications applet has duplicate entries

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