I have the same or very similar problem on Ubuntu 16.10.

It happens usually after certain programs are run (like notepadqq,
sometimes open office or image viewer and most usually Netbeans, with
Netbeans on it's nearly certain it will happen on my laptop after some
time running, especially when there are more programs). It usually
blocks Chrome from navigating tabs, sometimes other windows from clicks
or resizing. If not with Netbeans then usually when doing something
processor and ram intensive in background (but not as much intensive to
be low on memory, like having 16 GB RAM and using 6 GB and 100% of 2
processors).

Strangefully usually closing Netbeans help for me - but not always.
Sometimes it's ok after closing but problem is back in few minutes after
closing.

It looks like it might be related to some resource in the system but I
can't guess which one.

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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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