I had this problem also until I learned that you can add an EXTRA condition using OBJECT that is colliding to PICK INSTANCES using the Z ORDER where you can say for example pick the top one when many collide.
So:
1) OBJECT #1 collides with OBJECT #2
and 1 more condition: OBJECT #2 Z ORDER pick top/bottom > top
ACTION: badaboom badabang
That will solve your problem