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 Josh is telling Ben Stiller that the candy belongs to Seymour Butts, his lips don't match the words he's saying. In the next shot, Ben Stiller responds, and his lips don't match the words he's saying either.
Audio problem: On the way back to the house, in the back of the horse cart, Babe and Fly are talking to each other. They never open their mouths while they're talking.
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: 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.
Audio problem: Billy swings across the construction site to help Aiesha, he then stamps on some ooze men's heads. He counts each stomp up to 6 and we hear 6 stomps. However there are only 3 ooze men, and we can plainly see Billy doesn't stomp any more than once. (00:25:25)
Audio problem: When Max tells Fishman to get the hell out of here, his lips don't move.