The Man With No Name takes off on a brown horse after shooting the three baddies before El Paso. Then he rides into town and ties up a chestnut horse. Then the rest of the movie he is riding a bright bay with a blaze.
The Man with No Name (Clint Eastwood), after entering a place for something to eat and drink, holds up what looks like a plastic wreath, looks at it then throws it down back on the table. Plastic was not around in the late 1800s.
When the Baxters and the Rojos are shooting at each other at the cemetery, Ramón Rojos runs over the tops of the rocks to get a better shot. As the Baxters fire at him, there is one bullet that hits the rocks under Ramón that had no sound of a rifle being fired nor any ricochet sound.
When the large barrel rolls down the ramp, it rolls on two large rails. Right afterwards Joe crawls down the ramp, and no rails are visible. The large rails re-appear when his captors come into the room right after he exits.
While Chico carries The Man With No Name back to his room after the party, the camera shows The Man With No Name has no facial hair. Also, when the Man With No Name enters his room after the massacre, Rubio is a different actor; Ramón's mustache is parted.
The action before, during, and after the graveyard fight alternates between taking place during the day and night. The Rojos leave in pitch darkness, cut together with scenes of the Baxters riding out in cloudy daylight. The fight takes place during the day while Joe sneaks into the Rojo house at night. When the Rojos return home, it's night again.
When Joe and the Shop Keeper see the soldiers leaving town in the morning, the Shop Keeper is getting dressed and leaves his pants unbuttoned and shirt askew from center. Then the next scene in the same room his pants are completely button and his shirt opening is centered and buttoned up.
In one scene showing the hills beyond the town, the ruins of Tabernas Castle can be seen on the hilltop, showing that it was filmed in Andalucia, Spain. The castle was used by Fernando and Isabella during their siege of Almeria in the 1480s.
In the scene where the Mexican cavalry are ambushed at the river, the machine gun used by the 'US Cavalry' is unloaded at all times - it is a belt fed weapon, yet has no belt of rounds in it - it presumably has caps in the end to produce the muzzle smoke. Furthermore a hand cranked Gatling Gun would be more appropriate to the time line the film is set around than the slightly more modern air cooled belt fed weapon used.
When the Rojo gang ambush the Mexican army unit the gun Ramon uses to kill all the troops is a Mitrailleuse volley gun. Each barrel had to be laboriously loaded by hand before all barrels were fired together in a single volley. However, the film shows the volley gun being used as a form of machine gun. The only machine gun around at the time was the hand-cranked Gatling gun which the soundtrack also seems to depict.
When Ramon shoots the escaping soldiers, by the river, in their backs, he does so with a Gatling Gun. Yet, when the "shot" soldiers cry out and fall to the ground, no blood or even small holes can be seen in their clothes. A Gatling Gun would rip them (the soldiers, as well as their clothes) to pieces.
In the hostages exchange episode, when Marisol is still at the other end of the main street, Ramón tells her quietly, "Go to him, Marisol". This must be an error in editing as her child only runs into the street later.
After Joe sets off the dynamite, he's standing in the street where the strong wind is blowing to the right of the scene. Yet we see the buildings behind him, where the dynamite smoke is blowing to the left of the screen.
In the final fight at the end of the movie - he shoots 6 shots in total at the Rojo gang - then fires a 7th shot to free the man hanging on the rope without reloading. The revolver he is using can only fire 6-shots and then needs to be reloaded.