Continuity mistake: When Natalie Imbruglia and Rowan Atkinson are trying to enter John Malkovich's "chateau", when Natalie is climbing a ladder a tattoo is visible on her lower back. Later, when Pascal Sauvage (Malkovich) is being crowned, Natalie is seen fighting a sniper on the upper-level of the church. When the sniper pushes her away, the tattoo on her lower back is gone.
Continuity mistake: The first time the film of Johnny in the mirror is shown, look at the toothpaste in the bottom right corner. First you see the Aquafresh, then it cuts to Sauvage, and when it cuts back the toothpaste tube has moved. Then it cuts away and back again, and the toothbrush has moved in front of it.
Visible crew/equipment: In the hearse chase scene, when Johnny is getting out of the car, on the side view you can see a very obvious cover up of the camera in the window reflection.