Ray, this is a known issue and is tied into the development of the new fish behaviours/models. Once Jim achieves a breakthrough regarding said behaviour/models (into which is tied a more sophisticated collision avoidance technique), the coral passthroughs should become a thing of the past - or at least become extremely rare. We are all awaiting the breakthrough with baited breath, but it may take some time to arrive.
Meanwhile, have fun with the current aquarium secure in the knowledge that improvements are constantly being worked upon.