Other mistake: When Jill tries to leave Sweetwater in the morning after Cheyenne's visit, she runs into Harmonica. He has a very nasty, coarsely stitched injury in his cheek that is not accounted for, and for which there was no time to be received, stitched, and the stitches removed again. (Special Edition DVD has a deleted scene in which Harmonica is beaten up, which explains the injury, but it is a continuity mistake within the regular movie.)
Other mistake: In the scene in Morton's Special Waggon where Wobbles gets pinned by Frank ("A man who can't trust his own pants") Harmonica lies on the roof, not so unseen as he hopes to be. When the train leaves Flagstone Station you see a shot of Flagstone on the track's right. But on the left you see some far more modern housing. That is when see along the top of the train over Harmonica.