You may look at what the actual configuration is, and see if anything odd shows up. For instance, for my favorite app "Firefox" I would open a terminal and type:
Code:
bruno@LT_B:~> gsettings get org.gnome.shell favorite-apps
['firefox.desktop', 'evolution.desktop', 'empathy.desktop', 'gnome-music.desktop', 'org.gnome.Nautilus.desktop']
bruno@LT_B:~> ls /usr/share/applications/firefox*
/usr/share/applications/firefox.desktop
bruno@LT_B:~> nano /usr/share/applications/firefox.desktop
and look for missing or duplicate launchers (xxx.desktop files) or strange details shown by the editor (nano or your favourite one)
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