Same problem here. The way to provoke this is the following:
Open up some application - f.e. Libreoffice Writer
Do a few mouse clicks - everythin ok
Then  go to one of the hot corners
Then back to L-writer - mouse pointer is off.
In LO-writer minimize/maximize window and all is well again

Compiz is the culprit?

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https://bugs.launchpad.net/bugs/1612965

Title:
  Mouse cursor has wrong postition (Ubuntu 16.04)

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