I noticed that this happened when I have the option "Switch between
minimized windows" off from the Unity Tweak Tool --> Switcher Tab. It
seems to not happen now that I turned that on again.

I experienced this problem mostly on Chrome, but I guess it would happen
for other windows also.

The reason I had the option disabled is that it was a way to make the
"show desktop" hotcorner work. It doesn't work now but I prefer this
from missing the cursor.

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https://bugs.launchpad.net/bugs/1306550

Title:
  Wrong mouse-coordinates in the window after minimize/maximize of after
  return from  fullscreen

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