Factual error: Eight months after Craig has taken over JM and made him into a puppeteer JM's hair is much, much longer than it could have grown within that period. (01:25:00)
Continuity mistake: While JM is crawling through the mud of his own portal you see for a split second that he is wearing gloves, which he didn't wear before. (01:06:40)
Audio problem: During the Subcon Chase when Lotte and Maxine go through Malkovich and his date says 'You're creepy' she just nods and her lips don't move.
Continuity mistake: When Lotte is in Dr. Lester's house she's having a cup of tea. When the camera angle changes the handle of the cup switches from left to right. (01:17:00)
Continuity mistake: When JM talks to his friend Charlie about his strange experience, Charlie is playing with a Rubik's cube. The cube disappears from one moment to the next and is neither in his hands nor on the table next to him. (01:02:20)
Continuity mistake: In the scene after Maxine has made love with JM for the first time she is sitting on the floor in her office. The way she folds her legs changes depending on the camera angle. (00:56:20)
Visible crew/equipment: After the interview, when Craig and Dr. Lester are sitting on the windowsill, you see the shadow of the boom mike on the upper frame of the window. (00:11:30)
Continuity mistake: In the opening scene, when Craig plays with his puppet, the puppet hits a glass into a mirror. The mirror breaks and you see big pieces falling down, but in the next shot the glass is back in completely and just cracked. (00:01:45)
Continuity mistake: When Cameron Diaz is in the portal and Maxine is on top of John Malkovich on the couch, they keep on switching shots. One shot shows Maxine and John Malkovich and the couch, while the other is Diaz's view from inside Malkovich. The straps on Maxine's top are over her shoulder from Diaz's view, but they have slid down her arm from the other camera shot. (00:54:05)
Continuity mistake: When Craig is waiting at the New Jersey Turnpike roadside for Lotte, he is not wearing his glasses. When she falls down, from one shot to the next, he has them on again. (00:36:20)
Continuity mistake: When Maxine is having dinner at the Schwartz's the wine in Lotte's glass increases although no one has poured it. (00:50:05)
Continuity mistake: When Craig enters Maxine's office after he has been inside John Malkovich for the first time there's a coat hanging over the doorknob. It falls down as he enters, and he doesn't put it back. However, in the next shot, the coat is back hanging where it was. (00:31:10)
Continuity mistake: When Dr. Lester shares his fantasies with Craig while he's leaning on a filing cabinet, he's either talking with his left hand rested on his right arm (seen from the front) or with both hands held open (seen from behind). This changes several times. (00:17:30)
Continuity mistake: When the first customer comes and asks about what exactly is going to happen he breaks into tears in his low self-esteem. Then Maxine asks for the money, and from one shot to the next he is sitting straight, holding a paper with both hands. (00:47:30)
Visible crew/equipment: When Catherine Keener is being chased by Cameron Diaz, crawling through the cat flap and into the bus, a hand pokes through the flap and helps her through. (01:34:45)
Continuity mistake: When 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. (01:07:25)
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. (01:08:55)
Revealing mistake: When Lester moves in the tunnel for John Malkovich's mind, you can see the rope. (01:36:20)
Continuity mistake: When Maxine and JM make love the second time he realizes that someone else is inside him. When he confronts her she is sitting on a sofa, her blouse partly buttoned and one leg over a pillow. When the camera angle changes her blouse is totally unbuttoned and the pillow is on her lap. (01:01:00)
Continuity mistake: When Maxine calls the newspaper to submit the ad for JM Corp., she is sitting either normally or with one foot on the chair and her knee above the table alternately. (00:40:25)
