Hey BinarySteve any luck with this? I am experiencing the same problem on a mbp (el capitan) + external monitor setup with “displays have separate spaces” switched off. I never seemed to have this problem when “displays have separate spaces” was on.
Suffice to say it happens so often that I’m forced to have a permanent keyboard shortcut for restarting the dock. Sometimes the problem triggers a few seconds into mission control consistently so I’m forced to use other means to do what I initially intended.
ps it happens irrespective of hot corners as another user pointed out.