Other: 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.

Continuity: In the scene where John Malkovich goes into his own portal he suddenly is in a restaurant filled with himself.  If you look closely you can easily see that instead of carefully using computer graphics and superimposing his head on all the other bodies they just used extras. They got lazy and it is very easily seen that many of the Malkovich's are just older men that are balding and have grey and dark hair.