Some of my windows (for example libre office) have been getting stuck on the top left of the screen because Ubuntu Unity was appearing to eat the menu controls. I could not minimise, maximise or close the windows simply because the menu button weren’t visible.
The solution is to hold down the ‘alt’ key and drag the windows away from the top.
I didn’t know about alt-drag but is a really useful little tip.
Let me know if you find another solution.