Comment 5 for bug 774487

I see this with VLC too, so it's probably with any fullscreen app.

However, at least on 15.04, ticking the 'Always on top' option via the right-click titlebar menu of the video window is an effective workaround.

This seems to suggest it ought to be easy to fix? It's clear Unity can draw things correctly with the 'always on top' setting, so it seems like it just needs to understand that full-screen is very similar to 'always on top'.