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 Van Pelt is chasing Alan outside the house, he turns to shoot at Carl the cop. If you count the shots heard fired, there is one more hole than bullets heard. (00:56:15)
Audio problem: When Alan is trapped by the floor he is given a wooden log and then tosses it away. The foley artist forgot to add the thump of the log crashing on the floor.
Answer: The game is essentially "resetting reality" back to the point Alan was first sucked into the game. So it is undoing everything that has been done - including taking away the gun and bullets Van Pelt had purchased.