Deliberate mistake: When Sarah, et al are surrounded by the Goblins in Goblin City, the first cannon fires causing an explosion in front of some buildings, one of which has a hanging sign with scissors on it. Later, after the squatty Goblin says, "Hey! I just fired you!" another cannon fires causing an explosion, and the very same shot is shown, only the first one was flipped. (01:20:15 - 01:25:35)
Deliberate mistake: In the final battle where El Guapo's men are fighting the townspeople, look closely to see that they are really just fighting Lucky, Dusty, and Ned. When the towns people appear, their outfits are very different from the real Amigos.
Deliberate mistake: The filmmakers wanted a scene where Andi is startled by Max as he spacewalks behind her at Daedalus. Given that the only way to communicate in spacesuits is through radio, and the two suits would presumably been on the same channel with the shuttle, Andi would have known Max was coming. Further, even if they were on different channels, why wouldn't anyone tell Andi that Max was coming?
Deliberate mistake: When Howard is being sucked out of his planet by the laser beam the couch ignites but he doesn't.