Other mistake: When JM lands at the New Jersey turnpike he has an argument with Craig. When he walks away down the road a car drives by from behind. Someone in the car throws a can at him, shouting "Think fast, Malkovich.". This guy had no way of recognising him from behind.
When Craig first discovers the portal door his crouching position changes slightly between the camera shot inside the tunnel and that from the office, and again when he closes the office door and goes back to the portal door.