Revealing mistake: When they are escaping from the giant mosquitos, Peter shifts the car into 1st gear, not drive. (00:40:40)
Revealing mistake: During the monsoon scene, everyone is on a table trying to climb on the chandelier. Peter has been turned into a monkey, and his face is covered in hair and has the characterists of a monkeys face, yet in shots when they are on the table, like when the crocodile snaps at them on the table, just before Alan lifts Peter onto the chandelier, you can see the plain face of his stunt double, with no monkey features! Robin William's and Bonnie Hunt's doubles are rather obvious in these same shots too. (01:17:20)
Revealing mistake: During the monsoon scene, Sarah has both her feet aginst the jaws of the crocodile, and so Alan jumps from the chandelier, and dives into the water. As he dives into the water, watch Sarah's feet, and her left foot slips into the crocodiles mouth, and his upper jaw slams down on it! The crocodile has a row of sharp teeth on at the front of it's mouth, which come down onto her shoe. That would be painful, yet she doesn't scream/limp/complain. (01:17:55)
Revealing mistake: When Alan's face is stuck into the floorboards, after they had turned to quicksand, the boards assumingly go back to being hard and wooden, yet in shots of Alan talking you can see the boards bounce/wobble slightly, showing they are rubber. (01:21:45 - 01:22:45)
Revealing mistake: When Alan's merged with the floor and the first huge spider shows up, there's a thin wire coming out of its rear to make the animatronic move.
Revealing mistake: In the scene where Van Pelt sticks his hand out of the pile of paint cans you can see a can roll and bounce off of his extended fingers. A can of something that heavy would stop, not bounce off. Van Pelt's hand and wrist are shown covered in paint, so we know the can wasn't empty.
Revealing mistake: When the monkeys are in the garden, running away, just after Judy says "Beware", they cast no shadow either on the paved entrance, nor on the grass, plus they move as if in stop-motion, instead of the perfect movement they did before.
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.