Output of awesome --version:

awesome v3.5.9 (Mighty Ravendark)
• Build: Mar 7 2016 18:22:52 for x86_64 by gcc version 6.0.0 (mockbuild@)
• Compiled against Lua 5.3.2 (running with Lua 5.3)
• D-Bus support: ✔

awesome v4.0 (Harder, Better, Faster, Stronger)
• Compiled against Lua 5.1.5 (running with Lua 5.1)
• D-Bus support: ✔
• execinfo support: ✔
• RandR 1.5 support: ✘
• LGI version: 0.9.0

How to reproduce the issue:
assuming following config:

menubar.menu_gen.all_menu_dirs = { "/usr/share/applications", "/usr/local/share/applications" }

• install application (e.g. google-chrome)
• open menubar (super+p)
• start writing google - there is one entry 👍
• $ cp /usr/share/applications/google-chrome.desktop /usr/local/share/applications/
• restart awesome
• open menubar (super+p)
• start writing google - there are two entries 👎

If multiple files have the same desktop file ID, the first one in the $XDG_DATA_DIRS precedence order is used.

(https://specifications.freedesktop.org/desktop-entry-spec/desktop-entry-spec-latest.html#extra-actions-implementation-notes)