I had a couple of problems when upgrading my debian system after selecting gnome-classic interface (I since shifted to regular gnome3 desktop).
This is fairly minor, I ended up with 2 icons for GNU Octave.
A lot more annoying this one, I could no longer start Evolution (email client) from the start menu, instead I only had an option to change the settings for evolution. To solve this I had to start evolution from the command line. This problem seems to arise because we are expected to use the favourites panel.