collision detection on rocks ect is buggy to say the least my experience from others games tells me when collision boxes touch and overlap each other it can have a strange effect i.e boxes not fitting the objects, maybe this info will help.
It almost seems like the hitboxs are not box shaped but more like a cylinder or the hitbox for collusion is so small they never get a chance to collide.
We have mainly seen this on player vs player.
With terrain we have seen it with the new boulders.