Deliberate mistake: There's a bizarre editing gaff in the opening fight of the Director's Cut. At one point, Fasil's sword vanishes (for no real reason) and he starts to do backflips. The scene then cuts away, and when it cuts back, he's suddenly running and has his sword again. A few shots later, he's suddenly doing backflips and has lost his sword again. (It's meant to be Fasil doing the flips.) The editing makes absolutely no sense. It's like they somehow mixed up two different scenes during editing.
Deliberate mistake: The explosion of the ship at the end of the film is actually another angle of the explosion of the house from a few seconds earlier. The craft's explosion is much too small for what is shown in the film.
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.