When Sands first meets the bubblegum-selling boy, the shots of the boy have been flipped - the writing on the pack is backwards.
Before the guitar maker presents his work to El Mariachi, he is shown playing it left-handed. In the next shot, he is strumming right-handed. Then, as he hands it over to El, it is positioned as if he had just been playing left-handed again.
The chain tying El and Carolina together is removed with an electric wire feed welder (used for welding) and not a blowtorch (used for cutting), removing the links closest to the cuffs. When it falls to the ground, it is whole again.
When Agent Sands is being tailed by the cartel hit-man, you can see the small pistol in his hand before he pulls it out of his trousers.
When Sands takes off his jacket after being shot in the arm, there is no bullet wound. Later, a bullet wound appears on his arm.
When Ruben Blades meets with Johnny Depp, Blades tells Depp that there is no extradition between the US and Mexico. This is not true. The only time Mexico won't extradite someone to the US is if the person needing to be extradited is facing the death penalty.
The Gun that Ajedrez uses is a revolver with a silencer, but this model revolver can not be silenced.
The president wears the sash over his suit. The only time the president of Mexico wears the sash over his suit is when he is sworn into office.
When Sands gets shot in the arm toward the end, the squib is clearly visible.
As El Mariachi shoots at the thugs in the church, as he backs down the center aisle, squibs continue to go off behind the thugs even after El stops firing.
A number of times you can see Johnny Depp's open eyes (despite the makeup/dark glasses), after his character Sands' eyes have been removed.
After the gunfight at the end Jorge tosses a cell phone to Sands, who is leaning against a wall. Jorge doesn't say a word as he's walking by, he just waves the phone at Sands and tosses it to him. Sands catches it despite being blinded earlier.
At the bullfight, a cameraman is reflected in Sands' sunglasses.
The President says that Culiacan is a state in Mexico. Actually Culiacan is a city in, and the capital of, the state of Sinaloa. There is no state in Mexico called Culiacan.
El Mariachi and Carolina are young, and Carolina has been dead for about a year or so. So it is unclear how Marquez fits into Carolina's old love life since she and El had been together for years and she was with Bucho for several years before that.