Audio problem: After the "Off to See the World" part, it shows Klaus and Claudia in the pool. The waiter tells Claudia that there's a long distance phone call for her from Europe. "Wonderful!" Claudia says, and she slides off her raft and while she makes her way out of the pool, accidentally drops water on Sophie. The dog freaks out, trying to paw the water off her and Klaus snickers at her. After the shot of snickering Klaus, it shows Sophie turning her head towards Claudia and you could hear her bark. However, she does not move her mouth as if she's barking and the barking noise sounds quite perky.
Audio problem: The keyboard Kevin gets from the music shop seems to have an interesting trait, in that the high notes are on the left. This must either be bad "audio dubbing" or something to do with the shot perhaps being reversed, although I doubt this. It's most likely a post-production audio error as very very few keyboards or pianos are configured in this way.
Audio problem: In the mansion, the boys open a secret passage and fall through the floor. They scream after shining a flashlight on a skeleton. Eugene then can be heard whining that he wants to go home, but his mouth is not moving.
Audio problem: It's quite obvious that all of the grunts and sounds of terror that Ash makes while his hand is attacking him in the kitchen are dubbed. (00:28:45)
Audio problem: On the moon, Superman smashes Nuclear Man's head against his knee. The clonk is heard before the hit (even forgetting that sound can't be heard on the moon).
Audio problem: When trying to steel the BET, Serpentor fllies in close and Duke grabs onto his glider. The sounds of TIE Fighters are used for Serpentor's glider. You can even hear Darth Vader breathing for a moment. (00:15:45)
Audio problem: When Chatterer appears and shoves Frank back in the attic, we get a closeup of his teeth chattering, but when it cuts to a wideshot, he's no longer doing it. You could argue that he just stopped as the camera cut (a little flimsy, but arguably a valid correction), but the real issue? They continue to play the "chattering" sound effect for about a second after he stops even though his teeth are no longer moving. They try to mask it by fading it out quickly... but it makes the moment feel wonky.
Audio problem: After Wesley rescues Princess Buttercup from Vizzini, he takes her up on a windy mountain and they talk. In one angle, Wesley is talking and wind noise can be heard during his vocals. It never happens again during the shot although all shots in this sequence are windy.