Visible crew/equipment: During the scene where the girl is in the airplane with Martin Short, the plane is flying past some mountains. When the plane turns to the side, you can see the strings.
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: Dusty is dressed as one of El Guapo's henchmen. When Ned falls from the rope above and El Guapo's henchmen find out who he and Dusty are, Dusty is no longer dressed as a henchman, but back in his Amigo uniform.
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 the villagers of Santa Poco are making the Amigo outfits, the sewing machines are not threaded because no thread is seen in the cloth as it passes through the sewing machine needles.
Continuity mistake: At the start of the scene where Ned is fighting the German, Ned is given a gun to fight with and his own gun is put in the front of his pants. Later in the scene after he loses the gun given to him, he draws his own gun out of its holster on his side, not from the front of his pants.
Deliberate mistake: At the end battle where El Guapo's men are fighting the towns people, look closely to see that they are really just fighting Lucky, Dusty, and Ned. When the towns people appear, their outfits are very different from the real Amigos.
Factual error: The movie is set in 1914 and the German said he learned the "quick draw" from watching Ned's movies. The quick draw was not invented until 1950s TV westerns came along.
Other mistake: During the final showdown with El Guapo, three horsemen ride towards some fake Amigos and fall into a concealed ditch, throwing up their arms and falling off their horses. Unfortunately, they throw up their arms just before the horses even start to fall.
Revealing mistake: During their first confrontation with El Guapo, the Amigos start riding around and firing their guns in the air. Look at the difference in speed between the wider shots (with stunt doubles) and the closer ones, which show the actors themselves. Not only are they suddenly moving much slower in these closer shots, but it so very obvious that they are on mechanical horses by the movement.
Continuity mistake: When the bad guys are beginning their celebration just before the Three Amigos take them on, there is a scene where people are holding a series of ropes attached to a tall pole. About a minute or so later, when the Amigos are climbing onto the wall around the bad guys' compound, you can see all these ropes are suddenly hanging between the pole and the roofs of the surrounding buildings. How did the people get the ropes up there so quickly?