Factual error: After the birth of the baby, James Stewart and "Doc" Witherspoon are discussing the course of the war. "Doc" relates that he has always lived in Virginia and that his son died at Gettysburg at Little Round Top. No Virginia regiments fought at Little Round Top - only Alabama, Texas, Georgia, and Arkansas regiments.
Continuity mistake: Near the beginning when Lee Van Cleef looks at the the wanted poster on the ticket booth at Tucumcari (just after getting off the train), there are two extra zero's drawn onto the poster (as added by the villain). Van Cleef then takes this poster away with him, and slots it under the door of a hotel room on a later scene - notice that the additional zero's have since disappeared from the same poster. (00:06:30 - 00:09:20)
Audio problem: When the band is marching with the Massingale rally one can hear flutes and many band instruments, but the band consists of only a few brass instruments.
Revealing mistake: In the scene at the end of the movie where Lee Marvin is running interference during the escape by shooting in the air, horses pulling a beer wagon get startled and run into the street where the wagon turns over. At the beginning of the shot, when the horses begin to bolt, you can see the stuntman driving the wagon. He is sitting low behind the wooden front of the wagon (which has holes cut in it so he can see out).