I have the same issue. Sometimes programs don't react on mouse clicks, but 
mouse cursor working.
I have no idea how to reproduce the issue. But waiting a minute or so resolve 
the problem.
At the same moment keyboard, left favorites menu and activities work fine.

Seems this is the issue of gnome-shell because it has high load at the
moment of mouse locks.

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https://bugs.launchpad.net/bugs/1181666

Title:
  gnome-shell randomly blocks mouse clicks from working in app windows

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