Deliberate mistake: Bender goes back in time to two minutes before Fry came back to the past. But if you time it, it was actually only 1 minute and 42 seconds.
Deliberate mistake: During the fight on the ship, Lin and the others are holding Andre over the core before he falls into it. And suddenly the ship just starts exploding and crashing for no reason what so ever. It just suddenly happens to add tension to the scene. (01:33:45)
Deliberate mistake: During the final battle, at one point Sean kicks Crane off a rope bridge. When this happens, if you look closely you can see the rope railing on the side of the bridge fall away right before Crane falls. It's supposed to look like Crane is falling through the ropes, but they drop just a split-second too early (he's not even touching them when they start to fall), so it was done on purpose and mistimed. (It was likely timed to drop away just a split-second before Crane fell so that the stunt-person wouldn't accidentally get tangled in the ropes as they fell).