Gaffes

The chimp actor changes a few times - sometimes it has a white beard, while at other times it has no beard.

When Malkovich and Maxine are on his couch, the shoulder strap of her dress moves back and forth between resting on her shoulder or falling off her shoulder, depending on the camera angle.

When Craig Schwartz is about to enter the portal for the first time, he's kneeling. In the next shot, he's squatting.

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.

When Craig first wakes up ("wintry economic climate"), the position of the comforter around his shoulders changes several times.

Pressing "emergency stop" on an elevator wouldn't set off any alarms. It might alert security but one would have to hit the alarm button to sound an alarm.

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.

When Craig sees John's face for the first time in the mirror, the mirror doesn't accurately reflect John's point of view.

The same cars are driving past on the New Jersey Turnpike the both first and second times someone is seen appearing from the portal.

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.

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.

When Maxine enters Malkovich's subconscious for the gun chase, when the first smashes into the bedroom through the closet, there is a man in a green shirt on the left side by the chest of drawers. You can see his hands in one shot, then his whole body.

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.

When Craig gets spit out into a ditch for the first time, he is limping onto an on-ramp, a sign that reads "DOCK STREET NEXT RIGHT" is visible at the distance, suggesting a filming location at Terminal Island Freeway in Wilmington California.

When Craig and Dr. Lester are in the restaurant, two orange Los Angeles MTA buses pass by.

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.

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.

One logistical issue the film does not resolve is how Craig and Maxine are able to avoid severe sleep deprivation while simultaneously working 9 to 5 jobs and running J.M. Inc. from 9 pm to 4 am every night. This is especially true of Maxine, who seems to run the business every night (while Craig seems to spend some nights at home), and who also manages to maintain a series of dates and sexual encounters with Malkovich without ever seeming sleepy or exhausted.

It is never explained what happens to Craig's body while he is in Malkovich's body for an extended period of time.

The first time Maxine visits Malkovich's apartment, the shadow of the boom mic is 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.