Continuity: When Craig first discovers the portal, the hands of the clock on the wall (in the deep storage room) are fixed at 2:23 for several minutes.
Audio/visual unsynchronized: During the chase through Malkovich's subconscious, Lotte shoots at Maxine, who runs through a door. The shot hits the wall to the left of the door, but if you look to the right of the door, another bullet hole appears without any corresponding sounds.
Continuity: The shoulder strap of Maxine's shirt in the second love scene between her and John.
Errors in geography: When Craig and Dr. Lester are in the restaurant, two orange Los Angeles MTA buses pass by.
Continuity: As Craig enters Maxine's office to tell her of the portal there is a coat hanging on the doorknob. When he checks the hallway outside, the coat is gone, only to reappear after Maxine finishes taking her phone call.
Continuity: When Craig first wakes up ("wintry economic climate"), the position of the comforter around his shoulders changes several times.
Crew or equipment visible: When Lotte is chasing Maxine through Malkovich's subconscious, as Maxine drops into the school bus section you can clearly see someone's hand holding her skirt so she doesn't fall into the bus.
Continuity: When Craig Schwartz first boards the elevator, the alarm stops when the stop button is released, before the door closes. But when Maxine boards the elevator to descend from floor 7-1/2, the alarm keeps ringing until the door closes.
Revealing mistakes: When John Horatio Malkovich enters his own portal, some of "himself" (for example one he bumps into shortly before exiting) are clearly look-alikes or are wearing masks.
Boom mic visible: When Craig and Dr. Lester sit together on the office windowsill to have a conversation, the shadow of a boom mic is visible on the window frame between them.
Errors in geography: WALK/DON'T WALK signs in New York City at the time of the film used words. The camera zooms in on a sign where there is a upheld hand for stop and a walking figure for go. These pictograph signs were typical at the time in California, not NYC, where the movie is set.
Continuity: When Elijah the chimp lets Lotte out of the cage, he jumps out leaving the checked blanket all messed up. On the last shot of the scene the blanket is straightened out.
Incorrectly regarded as goofs: When Maxine enters the lift on the 7 1/2 floor, it stops there when someone calls it (from outside), but from inside you have to stop it with the stop button because that's how it works.
Continuity: During Craig's interview with Dr. Lester, the wound on Craig's lip moves, and at one point disappears completely.
Continuity: When Craig Schwartz is about to enter the portal for the first time, he's kneeling. In the next shot, he's squatting.
Boom mic visible: The first time Maxine visits Malkovich's apartment, the shadow of the boom mic is visible.
Errors in geography: Just after the first time Lotte falls out of the portal onto the side of the New Jersey Turnpike, a palm tree is visible in the distance over Craig's shoulder.
Continuity: The chimp actor changes a few times - sometimes it has a white beard, while at other times it has no beard.
Errors in geography: When Craig first lands by the N.J. Turnpike, there is an operating oil well in the background. There are no known natural oil reserves in New Jersey.
Continuity: When Craig runs his fingers over files, his wedding ring is on his right hand although usually it's on the left one.
Continuity: When Craig is about to discover the portal, he picks up the dropped file and puts it on the bureau next to him. But in the next shot that file is not there, only those that were there before.