Other mistake: In the very last scene of the movie, and just before Blondie shoots the rope that is holding Tuco on the grave's cross. You can see a car moving in the background, screen right of Tuco's head.
Factual error: When Angel Eyes arrives at the Confederate Army Hospital, the Confederate flag that is flying is not the correct flag; it is the flag that people in the 20th century and later think of as the Confederate flag. The only rectangular flag with the blue St Andrew's cross on red was the Confederate navy flag and the battle flag of the Army of Tennessee, which was the standardized battle flag for the Western Armies (but not that far west) after January 1864, so didn't exist in the New Mexico campaign, nor at the time the story takes place.
Revealing mistake: After the explosion blows a hole in the wall and Tuco joins the procession of people flowing down the street, when the shot switches to face the characters you can see that the 'woman' in a blue dress in the wagon is actually a man. (Time is for the extended version of the film).
Revealing mistake: When Tuco is about to shoot Blondie in the desert, and the Army wagon is seen approaching, the driver can be seen sitting far back in the rear of the coach wearing a hat.
Factual error: When Tuco and his associates come to kill him, Blondie stops cleaning his pistol and quickly loads it with brass cartridges, which were not available for pistols until 1873.
Continuity mistake: When Blondie and Tuco are planting dynamite to blow up the bridge, they are standing in the water. During the following blast, they are hiding away next to the river and from then on, they are totally dry again.
Revealing mistake: When Blondie is to be hanged by Tuco, and saved by a extremely lucky hit by a Union mortar, you can see that the wall that will be hit by the grenade has been has been blow to pieces at least once before; the bricks have no mortar between them, and there is a large circular scorched area on the brick wall.
Continuity mistake: Towards the beginning of the movie, Angel Eyes rides up to a house where he has to get information from a man inside and then kill him. After Angel Eyes kills him at the kitchen table, his son runs down some steps behind Angel Eyes in the background with a rifle in his hands. Angel Eyes pulls out his revolver, turns around quickly, and shoots him dead. Take note that the pistol is not pointing directly at the boy as he is firing it.
Factual error: When Clint Eastwood blows up the bridge, he lights only one fuse but all of the explosives detonate simultaneously, despite being attached to numerous, separate pilings.
Other mistake: Blondie suffers from severe sun burn wounds in the face, after the capture and dragging through the desert. The wounds look perfectly realistic, but disappear or change several times. The burns are completely gone shortly after leaving the monastery. Such burns would leave scars and traces for at least weeks.
Continuity mistake: When Blondie abandons Tuco in the desert, watch the rope around Tuco's neck. It changes between shots, sometimes over his left shoulder, and sometimes hanging down in front of him. It is not due to the camera angle.
Continuity mistake: When Tuco is riding his horse, he encounters three bounty hunters - one fires a shot making the horse misstep, and fall, bringing Tuco down to the ground. One of the bounty hunters ask Tuco, "Hey amigo, you know that you have a face beautiful enough to be worth $2,000.00?" He has a big blade of grass between his lips as he backs away from Blondie (Eastwood), however, there was no blade of grass between his lips when Blondie and he were close to one another. As he backed away, he had a rifle in his right hand and a wanted poster in his left, and he knew that Blondie had a gun pointed at him through his overcoat, so he was not able to put a blade of grass between his lips at any point.
Plot hole: In the scene when Tuco has ordered Blondie to stand on a stool and put the hangman's noose around his neck, he orders him to tighten the noose. Just as Tuco aims his pistol to shoot out the leg of the stool, an explosion causes the entire floor to collapse. Tuco drops to a lower level but logically Blondie should have dropped also, thus hanging himself. Instead he mysteriously disappears and lives on for the rest of the movie.
Factual error: When Tuco is in the gunshop messing around with the guns, one gun has the cylinder and barrel moving back and forth by manipulating the trigger guard-lever. This is a Belgian Galand & Somerville revolver, a gun that did not exist until 1868. This film takes place during the US Civil War, which ended in 1865.
Visible crew/equipment: When Tuco makes Blondie march through the desert, there is a shot at the very beginning and Blondie looks over his shoulder, feeling the strain of the desert. Then the camera focuses on Tuco and in this shot, you can see the tracks in front of his horse from a previous take.