Audio problem: During the end of "Prima Donna" when everyone sings "Light up the stage." you can see some actors and actresses singing the word "light" but you don't actually hear it until a few seconds later.
Audio problem: When Christine and Raoul leave the lair, singing to each other, she turns her head back toward the Phantom as we hear her singing 'each night, each morning,' but we can see she isn't saying anything: her mouth and lips aren't moving. It can't be that the Phantom is remembering the rooftop scene, because you hear the voices echoing in the cave, resonating differently as they move away. This is confirmed by the screenplay (p. 140 of "The Phantom of the Opera Companion"), which states that the Phantom hears them singing in the distance. (02:09:40)
Audio problem: Several times during "Masquerade", starting with the very first shot of the chorus singing, the audio does not at all match their lip synchs. (01:18:10)
Audio problem: In the opening song of Don Juan, Carlotta obviously cuts early, although her voice is still heard hitting the high (and obnoxious) note. (01:47:20)
Audio problem: Right after Firmin says "It would appear they've met before." Andre replies "Yes." However, his mouth and the words don't match up. (00:26:25)