I have the same issue on a new Asus Zenbook prime UX31A-R4003P.

For me, it seems that the problem appears when I use VirtualBox.
Suddenly, the mouse click does not work anymore on the laptop screen but
it works on my external screen (HDMI one).

If I click <<Alt>> key as said by Andrey Sidorov, this solves the
problem.

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https://bugs.launchpad.net/bugs/1077805

Title:
  left click stops working after a while

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