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.
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.
Factual error: The judges reading Tuco and Shorty's death sentences mention them being wanted by so many counties within "the state." This cannot be correct. The battles the characters are near at all times in the film depict the battles over New Mexico. The Union never invaded Texas through its western deserts, despite landing in the Rio Grande valley. New Mexico was not a state until 1912 and was never treated as a state by the CSA. Thus, the judges should be saying territory.
Factual error: The guns Tuco and Blondie use appear to be 1851 Colt Navy because they have octagonal barrels and the loading ram below the barrel. 2 problems are that 1) the '51 was only made in .36 calibre. When shown from the business end the muzzles appear to be much larger. Colt '61 / '60 came in .44 caliber, but they had round barrels. 2) More importantly they are using brass cartridges to load. Conversions for those pistols to load cartridges did not exist till after the war and these were cap 'n' ball only then.
Factual error: While cleaning his pistol Eastwood is using a plastic bore brush, not available in that era. (00:00:45 - 00:50:00)
Factual error: The movie depicts General Sibley's New Mexico campaign. This occurred in the first half of 1862, with the last battle occurring on June 1, prior to a Confederate retreat to Texas. General Sibley is seen, and he lost his battlefield command altogether in 1863. However, Angel Eyes makes reference to Andersonville prison, which did not open until 1864. The question is also begged as to how Art Scanlon, who died in February of 1862, had completely rotted away by May in dry soil.
Factual error: Regarding the train scenes when Tuco is taken then escapes from Mario Brega, there were no trains / railways in New Mexico in any of the years of the US Civil War, let alone 1862 when Selby's short-lived and daft campaign was limited to. I believe the RRs were starting to move into Texas then, but not NM until the 1870s. Also, the whole geography of the film is wrong if the gold was intercepted but 'escaped' with the three people in the wagon near Glorietta Pass in early 1862. The sequence of events means all involved had to go up and down the Rio Bravo constantly - eg. the 'jornado del muerto' is hundreds of miles from Glorietta. This is too complicated to summarise here, but check the actual battles and timelines.
Factual error: Extended version. After finding a dying Bill Carson, Tuco arrives at an outpost looking for a hospital. It's night, or at least dark outside - he is told the hospital is 18 miles away. In the next scene he arrives at the hospital at nearly high noon. A horse canters and gallops (full speed) between 4-30 mph. Basically the hospital was an hour away.