The Application Menu in the top panel, where the close/minimize icons are, are often wrong.
For example I use my email software (Lotus Notes), then I click on Chrome in the launcher - which puts Chrome in the foreground, however it still shows the Application Menu from Lotus Notes. Even while I am typing this question it still says "Lotus Notes".
It happens seemingly randomly on several applications. If I double click on the menu (to make the window smaller) then re-maximize it, then it goes back to the correct application menu.
Ubuntu 12.04 LTS with Unity. New Ubuntu user...
EDIT: I have 2 monitors. I've just noticed now that only 1 applications menu works correctly at a time. If I get the one on the main screen to look correct (using double-click steps mentioned above), then the menu for the secondary screen will stop working correctly. And vice-versa.