Continuity mistake: In one scene, Steve Martin is shot in the arm and bleeds, but when the trio return after the riot the wound has disappeared.
Continuity mistake: When the Amigos are deciding to "be the three amigos for real", Dusty is the last one to agree. Before approaching the other two, he grabs for his gun and it discharges, hitting the ground with the shot. Glass is then heard shattering in the distance. At this point, Dusty had not decided to be a "real Amigo", so his gun would either be loaded with blanks or unloaded, not loaded with live rounds yet.
Continuity mistake: When Lucky has El Guapo at gun point with the "Man's Gun" and the Amigos are making their escape, his ivory handled Colt is missing from his holster because it was confiscated by the bandits. Later at Santa Poco in the final battle Lucky has it back.
Continuity mistake: When the 3 stop to drink from their canteens, Ned gets sand and some mud on his face. When he looks at Dusty, there's now a darker mud stain on his right cheek that wasn't there before. And in the close up, the stain is gone but he has a lot more sand on his face, including all of his nose.