Continuity mistake: Indians are on a hilltop and a jet vapour trail can be seen in the sky.
Factual error: Near the end of the film Butch is complaining about the living conditions they have to endure - jungles, swamps, snakes, night work - and Sundance sarcastically retorts "Bitch, bitch, bitch!" In 1908 the term meant just what it literally means: "Female dog." It did not adopt its current meaning of "complain" until much later. At the time the film is set - outside the context of "female dog" - it was considered to be a serious obscenity, and it would not have been used to describe something as ordinary as someone moaning about his living conditions.
Revealing mistake: When McCullough is discussing Prudy's oddities with the matronly lady out front of the mayor's house, it is obvious that the lady is standing on a dirt-covered concrete sidewalk.
Visible crew/equipment: In the last scene, when they are riding alongside a river, shortly after the harmonica player changes songs, there's a closeup of John Wayne and appearing from the right on the other side of the river, a pickup truck appears, and then they quickly cut to different characters. (01:56:55)
Visible crew/equipment: In several scenes there are rectangular arrays of studio lamps visible, reflected in the actors' space helmets.
Continuity mistake: Sykes is shot in the right leg, in the thigh area, by the bounty hunters. We see the blood clearly on it when he sits on a rock and holds his leg. Later, when he returns to Aquaverde where he meets Robert Ryan, we see as he sits on his horse that his left leg is bandaged.
Continuity mistake: At the dinner scene when Mattie Ross is trying to obtain Rooster Cogburn's services, Rooster clears the table, and in the next scene he re-clears the table by pushing everything aside to play cards with Chin Lee.
Continuity mistake: At the end of the town collapse, a sincerely drunk Ben dives head-on into a tub where a lady (in her underclothes?) is just enjoying a bath. Propelled by Ben's momentum the tub with both passengers slides down the slippery planks and splashes into the river, while Ben rearranges himself into a comfortable sitting position between shots. If I wasn't completely mistaken also the lady changes her outfit, since the embroidery is missing when they float along. (02:23:35)