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.
Continuity mistake: When Van Pelt shoots the tire shelf in the store, the attached red wood triangle support is actually different between shots - note paint and dings. Furthermore, dirt marks on the tires appear, and two of the slotted heads of the screws, that are screwed into the anchor eye plate, are turned facing opposite directions (before it breaks). (01:09:25)
Revealing mistake: When they are escaping from the giant mosquitos, Peter shifts the car into 1st gear, not drive. (00:40:40)
Visible crew/equipment: When the police car gets dragged off by the vines, there are wires visible attached to the boot of the car. (01:18:00)
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.