Duplicate icons in GNOME Shell

In the Activities Menu, search for the "Main Menu" app, then uncheck or delete the categories you see selected under Debian. This removed every instance of duplicate low-resolution icons for me.

Edit: I'd personally delete whole Debian icons tree - this will make sure those items aren't appearing even though you unchecked them, because I found this feature (disabling icons) buggy. Although there was problems which I stated a while ago, this was still solution of my problem.

I found the answer in different place, just remove 'menu-xdg' and it will work.

It worked on my laptop, i removed it then restarted and every thing is great now !!!

Go to - /usr/share/applications/ as root. Find .desktop files and delete them. But don't forget to make backup of those files.