Plot hole: Captain Smolsky only gets hit in the back with the plaster. So why, later on, is his entire body covered in hardened plaster, like a mummy?
Plot hole: In the runaway train scene, Gene Wilder uncouples the train from the forward car, and has to make a dramatic leap to get back to the uncoupled car. Is there any reason he couldn't have uncoupled the train from the back car and just stayed put? It seems an unnecessary bit of drama.
Plot hole: In the final scene where they all leave along the passage; the father rolled out on a stretcher and the others casually walking out, you can tell by their smooth passage along the corridor that all the dead bodies have been removed, but this would have taken at least half an hour if not longer, so it would make no sense in reality for them all to wait for all the bodies to be removed before they left as they would have been the first to leave due to the traumatic experience they had just been through.
Plot hole: Since the criminals who used the dogs to rob the bank in the first movie were never apprehended (No criminal worth their salt would tell the authorities their caper was spoiled because the canines ran off with their loot), there is no way the people who are hunting the dobermans in the beginning of this movie would know the dogs were still carrying the cash. (00:18:00)