At the end of the opening credits song, the Mariachi raises his left hand to shield his eyes from the lights as he tries to see who's clapping, but the light is clearly coming from his right so his raised hand would not shield his eyes at all.
The Short Bartender uses a revolver with a silencer on the barrel. It is impossible to silence a revolver. Revolvers can't be silenced because there is a gap in the rear between the cylinder and the hammer, and a gap in the front between the cylinder and the barrel. A lot of noise from the explosion escapes through these gaps when a revolver is fired. Then again, on
one occasion, it does make the sound of an un-silenced gun, so perhaps the filmmakers were acknowledging that the silencer would not work.
In the scene when Bucho's right hand man puts his brother in a street fight to test his skills, Pito snaps his right leg above his ankle. Seconds later, his brother uses his right leg for an impossible roundhouse final blow.
On the rooftop of the bookstore, El Mariachi reloads one gun and then pulls another from the front of his pants but in the next shot he only has one gun, which he is loading, and has had no time to put the other gun away.
When Carolina jumps from a roof to another one, when filmed from underneath her, she seems to have light-color (e.g., skin-like or beige) panties. When she lands on the second roof, it is clear that she wears black ones.
After El Mariachi and the accountant slide toward each other on the bar they each fire their weapon (with both of them being empty). El Mariachi drops his gun on the bar and in the immediate reverse angle it is still in his hand, then switches back to the original angle where his gun is again on the bar.
When El Mariachi is on the bar, one of his band members flips is guitar over and drums on the back of it, in the next shot when El Mariachi is back on the stage, his band member is just flipping his guitar over.
When El Mariachi follows the boy and slides his shoulder along the wall, leaving blood smears, in one shot you can see what look like places where smears from a previous take have been not-quite-completely scrubbed off.
During the street firefight near the end of the film, When Campa drops down, and flips his guitar case onto his shoulder in preparation to fire a rocket from it, there is no opening or hole at all in the end of the case. The hole the rocket fires from does not appear until 2 shots later, after another shot of the approaching vehicle, then back to Campa. It is in this second shot of Campa that the hole appears and the rocket fires from it.
When the rocket that Campa fires at the bullet proof car reaches the vehicle, if played in slow motion, the rocket can fairly clearly be seen to hit ground just under the front bumper, spin slightly to one side and then continue to burn, while the car explodes, marking the "rocket" as nothing more than a simple firework rocket of some kind.
The goof items below may give away important plot points.
Danny Trejo (knife thrower) is shot several times by one of Bucho's guards on his chest right on his famous tattoo. When they examine the body, they open up the jacket; there is only blood, no bullet wounds.
At the bookstore, when the Mariachi and Carolina run down the stairs with the intent of leaving the building, there is no smoke coming through the door and they are both completely oblivious to the fact that the entire bookstore on the other side of the door is on fire, right up until they open it.
After El Mariachi has thrown his guitar case away, they reverse back in the car and he opens the door to reach down and pick it up off the road. With the height of the seat and the fact that the car has raised suspension, there is no way he would be able to do this.