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.
Revealing mistake: At the start of the hearse chase, when we first see the bad guys pull a hand-brake turn through 90 degrees in a small London side-street, if you look on the ground you can see the skid marks from what must have been the previous take.
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.
Other mistake: When Bough is telling Johnny and Pegasus about the two criminals working for Sauvage, he calls Vendetta "Klaus", and indeed, the screen in front of them shows this. However, the end credits put his name as "Carlos".