Other mistake: When the three men meet Harmonica at the railroad station, Woody Strode removes his duster and the shootout occurs. When Harmonica meets Cheyenne and his henchman at the outpost, they are wearing three dusters, each with a bullet hole in them. How could there be a bullet hole in three dusters when Woody Strode removed his before the shootout?
Factual error: As Martha is lying the table near the beginning, she is singing Danny Boy. The song was published in 1913, long after the time period of the movie.
Continuity mistake: When Jill arrives at the McBain killing scene a close-up shows her looking in shock at the corpses. There are long, untidy strands of hair hanging down from both temples. When she gets off the cart, only the hair on the right side is loose. (00:45:20)
Continuity mistake: When Frank comes to the train to find all his men dead there's one of them in something like a kowtow position with his hands reaching back. When he is seen from the other side the hands are in front. (02:07:25)
Other mistake: At the end of the post station scene Cheyenne says to Harmonica: "Cheyenne's men don't get killed". The subtitles read "Cheyenne's, man, don't get killed", whatever that is supposed to mean. (00:42:30)
Continuity mistake: Cheyenne shoots a man through the tip of his boot. When we see the boot next, that is a little later when he and Harmonica check the station construction site, both his boots are intact. (01:28:50 - 01:34:20)
Factual error: If the movie takes place in the 1870's, then the hanging of Harmonica's brother had to have occurred at least 20 years before. Frank and his crew wear gunbelts with cartridges, an item not generally utilized until 1871.
Continuity mistake: In the train shoot-out Cheyenne shoots a man through his boot. When the boot appears first in the window it has a round tip, but when the gun goes off the tip is flat, as if it were pressed against the glass, only that the window has no glass. (01:28:50)
Continuity mistake: When Frank's henchmen wait for Harmonica at the train station it's very windy. For example, you see the wires of the telegraph machine moving, and a string that's dangling in the window behind it is swaying wildly. Only in two shots, when the station agent gets locked up, the wires and the string are absolutely still, to start moving as before in the next shot. Desert wind wouldn't stop completely just for a few seconds. (00:02:40)
Character mistake: In the saloon on the way to Sweetwater, where Harmonica meets Cheyenne and his gang for the first time, Harmonica grabs one of the men's coats and looks at it, saying "I saw three of these dusters a short time ago. Inside the dusters there were three men. Inside the men there were three bullets." Actually, while the movie starts off with the three men at the train station wearing dusters, in the shootout scene, the black cowboy is no longer wearing a duster. Harmonica would have only seen two dusters. (00:41:50)
Continuity mistake: In the final shootout, Frank slumps to the ground and Harmonica approaches him. Harmonica has the instrument in his left breast pocket attached to a cord around his neck. He pulls the instrument from the cord quite forcibly causing the cord to whiplash back and lie on his left shoulder. The camera then switches to Frank having the instrument forced into his mouth and then Harmonica comes back into view. The cord is now missing.
Plot hole: On her first night alone on the McBain farm, Jill hears someone playing a harmonica out there in the dark. She blows out a candle (but there is still plenty of light in the room), grabs a gun, positions herself at the brightly lit window, and shoots when the sees tha harmonica player lighting a match. This behavior is way too foolish for a women depicted as street-smart as Jill. (00:55:30)
Continuity mistake: Jill's arrival by train is quite badly edited: When she gets off, two porters carry her luggage to the station building. She looks at the station clock which shows 7:55, then down at her watch wich shows 10:10. This may indicate how the time has passed, but it looks strange. In the last shot her luggage is back at the tracks, and the porters pick it up again. (00:26:15)
Continuity mistake: Towards the end, right before the shootout, the hole in Harmonica's shoulder is suddenly gone altogether.
Visible crew/equipment: When Fonda and his men leave the train on horseback, after capturing Harmonica guy, the whole ground is covered with automobile tire tracks. (01:29:36)
Other mistake: When Claudia Cardinale first gets off the train station clock has the time as 7:55. When she looks at her watch the time on it is around 10:10.
Factual error: The camera rises up the side and over the roof of the Rail Road Office. The roof of the RR office looked like it was 100 years old. It would have leaked like a sieve all over. That RR office would have been a beautiful new building as it was on the interior scenes at that time.
Factual error: Cheyenne says his mother was "a whore in Alameda..." Alameda was founded in 1853 and incorporated 1854. The story takes place in the 1870's. Jason Robards was 46 in 1968. His character could have been not much older than 20.
Other mistake: With Harmonica secured in the train, Frank states he will handle 'the woman' personally. As he rides off with some men while the train pulls away, in the foreground modern vehicle tyre tracks can be seen in the dirt. (01:30:00)
Continuity mistake: When Harmonica tells Cheyenne about the three men he killed at the train station, he is sipping from a cup. He is holding the cup in both hands with his fingertips touching, but in the last shot he is holding the cup by the handle. It's theoretically possible but looks wrong. (00:42:10)
Answer: The movie was filmed at multiple locations in Spain and Italy, and also in Utah. Chances are they filmed out of sequence and made minor changes to the script later in the movie. There are many things left unclear in the movie, for example the same scene at the cantina/store, just after Cheyenne's crew shows up, he refers to Harmonica by his name when no-one said his name up until that point.