Can you tell us how your monitors are setup? Which resolusions to they have? How are they aligned?

Created attachment 199675 [details]
Screen Layout

We tested a bit on IRC, and we found that creating a pointer barrier like:

  Main.layoutManager.bottomMonitor
  global.create_pointer_barrier(r(0).x + r(0).width,
                                r(0).y + r(0).height - 1,
                                r(0).x + r(0).width,
                                r(0).y + r(0).height);

didn't stop the pointer. Offsetting in other direction ( y + height, y + height + 1 ) stopped it somewhat, but also stopped triggering the message tray sometimes, and the pointer still got through sometimes. Changing y2 to be y + height + 5 seemed to fix the pointer getting through.

This is actually a bug in the X server which shall be fixed when http://patchwork.freedesktop.org/patch/6785/ lands.

The problem is that the CRTC pointer constraining logic is off by 1 pixel and lets the pointer get 1 pixel further down than it should (and to the right too).

*** Bug 663814 has been marked as a duplicate of this bug. ***

This should be fixed in X server 1.11.3 so I'm closing this bug.