Audio problem: After the aeroplane crashed, a dinosaur stepped over it and the windows shattered making the typical sound of made-of-glass things when broken. They are made of plexiglass (a sort of fibrous plastic).
Audio problem: On the first level of the video game, after Velma brings up what she remembers what Eric said about the Scooby snacks in the game, you hear Daphne talking but you see Velma's lips moving. (00:01:00)
Audio problem: When Monica runs back upstairs to see what David did to her perfume bottle, the sounds of the footsteps on the stairs don't sync up with the steps we see her taking. (00:24:40)
Audio problem: During the "Sparke Motion" dance scene, the dance instructor is mouthing the wrong words to the song the girls are dancing to. "West End Girls" by the Pet Shop Boys was originally going to be the dance number, and that is actually the song playing for the recording of the scene. Richard Kelly couldn't get permission to use it, and "Notorious" by Duran Duran was substituted. The teacher is plainly mouthing words from the wrong song.
Audio problem: When the MVA agents confront Yulaw in the hospital, Funsch locks in on Yulaw's right shoulder first. His gun's sights show up, being blue, and then turn red. There is a sound that the gun makes before the sight vanishes. The shots change, and you hear the sound end while the site is off screen showing the scared doctor. Then, several seconds later, it shows Roedecker's gun lock in on Yulaw's left shoulder, and the sound happens as the blue site turns red, and vanishes. However, the site from Funsch's gun is still on Yulaw visible and red, only now vanishing. The sound it made already indicating that it was gone, but it wasn't. (00:33:25)
Audio problem: When the guy in Jack's truck says "You better pay for that camera", his mouth doesn't match his words.