Deliberate mistake: When Sonya finishes Mileena, Mileena's shoulders are muddy and she is face down, but when we have a close up of the dragon tattoo the right shoulder is cleaned off and what mud is left is dry. (00:42:25)
Deliberate mistake: When Jade is killed, Kahn is holding her up by her neck about a foot above the ground as the monster appears behind her. Right before the monster bites down and eats her, Kahn lets go over her neck... and she just sort-of floats in place. She should have fallen back down given she was being held above ground. (In all likelihood, the actress was standing on a box or something to make it look like Kahn was holding her up.) This happens a bit quickly, so it can be hard to catch.
Deliberate mistake: During the opening fight between Rayden and Kahn, at one point Kahn is kicked and lands on the ground in front of his generals. A few seconds later, he is hit and lands on the ground again... in the exact same spot, landing in the exact same position. (Watch for the somersault he does.) It's clear these are two different takes of the same stunt. It wouldn't necessarily be a mistake, except when he gets hit the second time, he flies backwards a bit, so it makes no sense for him to land in the exact same spot as before. Sloppy editing.