Continuity mistake: During the rooftop shootout Banderas reloads his gun (right hand one), than he takes another gun (the one in his belt) with the left hand. After a cut, Banderas reloads his right handed gun again and the left handed gun disappears.
Continuity mistake: When Bucho was smoking his cigar in bed, it goes from small to big and when he puts it on the ash tray, it's small again.
Continuity mistake: At the beginning of Desperado, El Mariachi has a flashback to the time when the white-clad druglord Moco shot his hand. There are obviously three mistakes with this scene, although the director tried to tally it with the one at the end of El Mariachi (1992). Firstly, Moco is much plumper in the flashback than he really was in the prequel itself. Secondly, the dead body of Azul, the original guns-in-a-guitar-case murderer, is missing from the ground. And lastly, it's obvious there's no blood on Domino (the dead woman)'s body; only smeared on the ground.
Continuity mistake: During the bar gunfight, Banderas is shown shooting on top of the counter but somehow winding back up in the same place twice.
Continuity mistake: When El Mariachi's friend goes to fire his rocket-launcher (disguised as a guitar case), at first, there is no hole in the case for the rocket to shoot out, yet a shot or two later, the case has completely changed, and now has a large hole in the front for the rocket, a covering flap for the hole and a hole for exhaust in the back.
Continuity mistake: The guitarists weren't going with the sound of drumming on their guitars. Also the timing of their lips while singing were wrong.
Continuity mistake: In the bar gunfight scene (where Cheech is the barkeep), Banderas and the bookie from the back room end up on the bar with pistols pointed at each other. Banderas puts his weapon down, then two camera cuts later he puts it down again.
Continuity mistake: When the knife throwing assassin is after El Mariachi, he throws the first knife at his left arm and the second one at his right hand. Then we see El Mariachi going around the corner, with most of his back out of view, as the assassin throws the third knife at him. A few moments later, we see El Mariachi taking the knife out of his back - it's right next to his shoulder, and it was impossible for the assassin to hit it from where he was.
Continuity mistake: When Antonio Banderas runs over the guy at the end of the big shoot near the end of the movie, the guy getting run over has been replaced with a dummy. You can tell because of how easily it moves and how much it twists. You can also slow the film down to see that the dummy's plastic hand is visible.