Also happens to me on 12.04 in Gnome Classic Mode from time to time.
Happens to plugged devices or integrated touchpads too.

Using the context menu click and left clicks in some wild fashion may
release the stuck focus, but no clear picture what event exactly
releases the stuck focus.

Triggering of the problem maybe involves wheel scrolling events or
conetxt menu usage in some unusual combination.

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https://bugs.launchpad.net/bugs/362359

Title:
  Focus gets stuck to a window - impossible to select other windows

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