You say this is an animation... do you have keys for the positions of the rocks that you may have not meant to do? I haven't tried animating the parameters of the Replicator, so I'm not sure what it would do. (Or if it can.) Check for any unwanted keys in the timeline. (Maybe you moved some rocks after moving the timeline pointer, leaving 2 diferent positions for the rocks, and Carrara did the tweening without you realizing it.) Good luck!