This is an extreme situation. However it is rather easy to get into this condition. A way to help manage the problem of revealing the replication surface, you can move the hotpoint of the replicated object to a location outside of the replicated object. Carrara will use the hotpoint as the connection to the surface. When you move the hotpoint outside of the rock, it will put the rock off the surface a little bit. Then, you should select 360 degree rotations in all three directions (x, y, z). The result is as follows.

-Kix