Workaround:

rmmod usbhid ; sleep 1 ; modprobe usbhid

This clears the problem. Also tried rmmod hid_multitouch and psmouse,
neither of which seemed to do anything. I don't see how this could be a
kernel module problem, however. Seems more likely that removing the
module resets something in gnome-shell.

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https://bugs.launchpad.net/bugs/1683122

Title:
  mouse input permanently locks to a single window

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