The book store has been burnt down, and Antonio is on the roof with Salma hayek watching Bucho and his men. Antonio can't shoot him 'cos it's his brother, so he turns in anger and walks away- Salma chases him. On the wall their facing, really quickly, you can see a boom shadow from the boom operator!
There is a low budget Spanish movie called "El Mariachi" that this movie was based on. The guy that shoots El Mariachi's hand works for Bucho but he never knows that because in the first movie, after he shoots through his hand, El Mariachi kills him.
To the comment of shouldn't have Banderas known Bucho was his brother: Not if Bucho sent some men to shoot his hand and kill his girl. Thus, he hunts down the man that sent the killers.