Continuity mistake: In the final scene at the sheriff's office, Mitchum has his feet up on the table top, and the boot soles are clean. But after Wayne walks out, there is suddenly a spot on a boot sole. (This is visible in the video)
Factual error: The town of El Dorado is located in Texas, as evidenced by the Texas county map on the wall in the County Sheriff's office. However, while on their journey to the town, Thornton and Mississippi shoot at Saugaro Cact, which is only found in the Sonoran Desert in what was then Arizona Territory.
Continuity mistake: As the sheriff returns from getting 'his evening bottle', the camera view from the rear shows his hat brim turned up. But when the view changes to the front, the brim is down. this change happens twice.
Continuity mistake: When Mississippi and Maudie return to the jail to deliver the news of Thornton's capture, and when Maudie begins to tell her part of the story, part of the veil she is wearing slides off her left shoulder. In the close-ups on the actress, the veil stays down, but in the far-off shots the veil is again draped over her shoulder.
Revealing mistake: During Cole and Mississippi's night patrol, a bunch of horsemen start making a fuss in the street. When Mississippi dives under their horses, there is an interruption between when he dives, and when he (supposedly) lies in the horses' path. Evidently, this scene was made by joining two cuts.
Factual error: Josephine, shooting from above, hits Thornton somewhere around his hips, in the area of his lower thoracic or upper lumbar region. The bullet is never removed, and Thornton has trouble later with his right hand going numb. A bullet pressing on the spinal cord in the area where he got shot would impact his legs and feet, not his arms and hands.
Continuity mistake: When Cole throws the bucket of water on J.P. in the jail, J.P.'s shirt is soaked but his left arm is dry. His left arm changes back and forth from dry to wet.
Continuity mistake: During the gun battle at the church, the bad guys are up in the bell tower shooting down on John Wayne's good guys. This is taking place in the middle of the night, but when the camera pans up towards a bad guy being shot in the tower, the sky behind him is obviously bright blue.
Continuity mistake: When JP is shot in the leg, it is his right leg that is shot and the younger doctor is tending to that particular leg. Then in the final scene, JP is using a crutch on his left side and using this right leg. He is favoring his left leg as if that is the injured one. (01:57:00)
Character mistake: The bartender in El Dorado was John Mitchum - Robert Mitchum's real life brother. "Elmer" was the character name of the bartender, as mentioned twice in the first saloon shootout mid-way through the movie and in the movie credits under "Elmer, Jason's Bartender." Robert Mitchum mistakenly calls to the bartender, "freeze it right there, Johnny" (inadvertently using his brother's real name, "John, " as opposed to his character's name, "Elmer") in the final saloon shootout scene. (01:20:59 - 02:00:22)
Character mistake: Mississippi is about to go out the door after some men but Cole stops him. A fight ensues and Mississippi shoots the men with his shotgun. Cole then has an attack with his arm because of the bullet in it. Mississippi says, "Cole, what's wrong?" Mississippi knows that he has this problem so it makes no sense for him to ask what's wrong.
Continuity mistake: Opening scene, JP confronts Cole in the wash room. Cole's collar is visible in the mirror. Sometimes it is nice and neat and sometimes messed up.
Factual error: The red chilis hanging in many scenes were developed in 1894 at University of New Mexico. They were not in Texas until the 1920's.