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.
Visible crew/equipment: When the limousine explodes (flying several feet into the air) after being hit by the second rocket, in one or two shots (most noticeable right before it explodes, during the rocket POV shot), you can see chains attached to parts of the limo, that were not there in previous shots. This has to do with the original idea, which was to have the car flip over in a deliberate direction when it exploded.
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.
Audio problem: 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.
Visible crew/equipment: After Bucho's men bring the dead knife thrower back to their ranch, when Bucho enters the limo, the boom operator and boom are visible, reflected in the limo window. (00:55:25)
Revealing mistake: When El Mariachi's one friend first fires a rocket at the bad guy's limousine in the climactic battle, you can see that the rocket itself never explodes, despite the side of the car blowing up. The rocket simply lands next to the car, and then remains there in plain sight whilst the side of the car blows up, revealing that it is just a prop replica.
Other mistake: During the bar gunfight, Banderas shoots the ventilator that falls down on the bad guy. In the next shot, you see that the ventilator is still rotating. The ventilator should be disconnected after falling to the floor, since the wire isn't that long.