Comment 2 for bug 778538

Maybe this is also a compiz bug, worsened by unity and its way to place the close buttons of maximized windows on the top panel. This could cause confusion by not knowing which maximized window is focused.

Possible fix:
(Ubuntu Forums - July 24th, 2007)
1 - First I went System>Preferences>Windows and turned on 'Select windows when the mouse moves over them', and set the 'Interval before raising' to 0.5, although I don't think the number is important.
2 - Then I logged-out and back in again to restart the window manager.
3 - Now when I mouse over an inactive window the window is highlited... clicking it focuses the window. This is nice, and I could get used to it, but not what I wanted. ...So I turned it off.
4 - Turning this on and off actually fixed the problem.
source: http://ubuntuforums.org/showpost.php?p=3071659&postcount=11

I turned on 'Select windows when the mouse moves over them' and it avoided the focus mistake issue, but I didn't try the "turn on and off".