Factual error: When Clint Eastwood catches an Indian arrow in his left shoulder, he instructs Shirley MacLaine to prime the arrow shaft with gunpowder, which he then ignites as she forces the shaft all the way through his shoulder. Presumably, the burning gunpowder would cauterize the wound all the way through his body, or that's what the filmmakers asked the audience to believe. In reality, gunpowder is historically well-known for causing gangrene in open wounds. With a shoulder full of gunpowder cinders, Clint Eastwood should have died of gangrene and sepsis by the end of the movie.
Factual error: MacLaine and Eastwood enter a small village, they dismount from their rides and start walking up an embankment. The background is an open air shot revealing the sky, Noticeable in the background up in the air are 12 high voltage power lines running across the width of the screen. Don't think those would've been there in mid 1800's outback Mexico.
Revealing mistake: The rattlesnake Hogan kills in the mission's ruin is fake: Its frontal part moves unnaturally stiffly, and its tongue does not flicker. (00:16:40)
Revealing mistake: After Clint has shot the 3 would-be rapists, he is rifling through the pockets of the dead men. As he checks the pockets of the first guy he shot the "dead" guy in the background is breathing.