As a former contractor, if it is not written down and signed, then any agreement made does not exist. On the other hand, if I messed up and installed a door that swings the wrong way, I should fix it. The best way to deal with this IMHO, is to talk it over with the contractor, and give him the oppourtunity to make it right.
As for the split trim, that should have been replaced no questions asked. With air nailers it is rare to split trim from nailing.