Thanks for uploading the saved game. I could not find any Pompey Assassination end of turn CTD issues, and I could not find the issue concerning Vorenus that you described. I garrisoned Vorenus, and then un-garrisoned him over a period of turns, and he never cloned or died as you described.
Concerning Julius Caesar being in a ship at end of turn causing a CTD that is in fact a problem. Thanks for bringing it to my attention as I did not realize that would happen. The cause of this problem has to do with the piece of script that automatically retrains his army at the end of turn. I'll try to find a way to modify that piece of script to prevent this CTD. If I can not find a modification to the script that will fix this CTD I'll probably have to just remove this piece of script altogether.