When Crosby is preparing to deliver Powers' baby, he has whiskey poured over his hands "to sterilize" them, a trick he claims to have learned in the Civil War. Surgeons did not start to wash their hands until after the Civil War, and during the war would routinely go from gut wounds to limb wounds and back to the trunk, merely wiping their hands between. Bacterial infections were still unknown by the medical field. Therefore, there would be no reason to sterilize one's hands.
During the opening attack, some of the Indians' horses appear to be shod. They didn't do that to their horses.
Inaccurate cavalry flag. In the Flags of the World website there is a section on US cavalry unit flags entitled Army - Cavalry Guidons (U.S.) . To summarize, a guidon is a technical term for (among other flag types) a fork tailed flag carried by each company or troop of cavalry. The regulations of 1833 made them divided red above and white below with a white "U.S." above and a red company letter below. The regulations of 1862 specified the design as a variation of the United States flag. The regulations of 1885 specified divided read above and white below with a white regimental number above and a red troop letter below. If the film is in 1880 the guidons should have a stars and stripes pattern but instead are divided, red above and bright yellow instead of white below. There are literally hundreds of other examples of the use of anachronistic or inaccurate guidons in movies.
During the Indian attack when the view is from above and the camera pans to a helicopter shot, you can see the shadow of the helicopter briefly at the top of the screen, behind the horseback riders. This occurs around 1h29m into the film on some prints.
During an Indian attack, when the stagecoach goes through a long puddle of water, fresh tire tracks can be seen on the left as the camera starts up to match the movement of the stagecoach.
After the perilous night-time ride down the muddy mountain during the rainstorm (and for that matter all throughout the movie), everyone's clothes was perfectly clean and pressed, as if they'd just stepped out of Wardrobe.
In the final chase scene, as Ringo mounts the lead horse of the stagecoach team, he is obviously wearing sneakers instead of his cowboy boots.
In the final shootout scene, Ringo shoots down a chandelier. The chandelier starts falling before the sound of the gunshot is heard.
When they stop to rest the horses and the Stars are talking, in the background a bus or van appears and drives through a fence gate on a dirt road.
The Native American Indians would have shot the horses to stop the stagecoach.
Whilst driving the team, Slim Pickens calls out the horses' names, but even after a change of horses he calls out the same names.