Comment 4 for bug 1161423

Removed software-center from affects list as it has nothing to do with this. Marked as incomplete as 2 people have stated it works as expected.

If you've got the .desktop file for the app in ~/.local/share/icons/ then it was not added there by a package. But was added by selecting to add the integration when visiting the site in Firefox or Chromium. Packages should not and cannot touch files in user directories, only system files. You will need to remove any per-user configuration on your own.