Audio problem: In the final fight scene between Liu and Shang Tsung, Liu hits Shang in the face repeatedly, but there is one extra hit sound for which there is no motion.
Audio problem: There are several times throughout the film when Miss Minchin is playing her harp and her finger movements does not match with what we hear.
Audio problem: When the Bat Exterminator is pointing at the book in the attic, he says "Some kid said she saw a bunch of those back in the 60's." His mouth is visible in the screen, however it doesn't move at all. (00:18:50)
Audio problem: Another audio problem in the same scene: As Brian Engle is approaching the cockpit, there is some more muttering, presumably in this order (using actors initials: MLC: Right, Good God. PW: Is he (muffled) MLC: I know, I seem real strange. He's outta control.
Audio problem: When Marie is hearing the sword fight in the hall, any shots showing her bedroom door show flashes under it corresponding to the sounds of the swords hitting. They are timed perfectly the first time and for the first part of the second time. When Marie gets up to go look, you hear a pause in the sword fight as you hear the Mouse King and Nutcracker struggling for a moment, but no sword clanks. Yet the flashing under the door continues.
Audio problem: When Andy is in his cardboard Buzz costume, and says "Buzz Lightyear to the rescue, " his mouth doesn't move.