Continuity mistake: When Pascal's henchmen infiltrate Buckingham Palace, and force the Queen to abdicate, if you look very closely on the abdication document it is dated the twentieth of March 2003. Yet in an earlier scene where Johnny English is photographed by the speed camera that has the date 21/03/03, obviously the abdication was filmed before the car chase, and therefore the dates get mixed up.
Other mistake: In the chase scene, where Johnny and Bough are chasing the hearse, when Bough and Johnny are discussing where the hearse went, Johnny says "They were heading south." Then he turns the steering wheel to his right, yet when it shows a view of the truck it turns to it's left. (00:22:15)
Factual error: When Johnny and Lorna are in the sushi bar, Lorna says 'cheers' in Japanese to Johnny before drinking Japanese sake. (An English subtitle is displayed). Johnny, obviously not knowing what he is saying replies in Japanese, and an English subtitle is displayed saying 'may all of your daughters be born with three bottoms'. The actual translation for what he says is 'May all of your daughters be born with a small penis'. (Not that any normal person would notice) (00:36:15)
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.
Deliberate mistake: When you see one of Pascal's henchmen turn off the power, he is wearing a black suit. In the reflection of the glass on the power box, you can see 'Police' written on the jacket. The filmmaker chose this suit because it was black, thinking no one would see the police logo on it.