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: When Josey gives the redlegs a "Missouri boat ride" by shooting the tow rope on the ferry, the craft drifts off down stream, silhouetted in the setting sun. The problem is, Josey and the kid are on the east bank, instead of the west bank where the Indian nation is located.
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.