EDIT:
After using your test file I can see most of my suppositions are incorrect. It does seem to be very simple.
Original Post:
I have this same problem as well. It will occur when zooming in some linked subplots but not others. It will also occur when brushing some subplots but not all the time.
I haven't figured out any way to fix it though and doing things like removing the legends doesn't seem to help. Removing the linkedaxes does not help either.
It will also occur after totally normal operation for a period of time and end up completely failing just showing the grey selection box whether or not the mouse is pressed and doing nothing. I'm still trying to create a 100% foolproof way to recreate the different errors.
My best guess at this time is that some zoom or brush action is still looking for the old subplot handle and when it is removed and replaced by a new subplot an error may occur.
Another strange aspect is that sometimes it will give that error but still work successfully as long as the subplots haven't been removed while they are zoomed in.
