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.
Factual error: After the Crown Jewels have been stolen Bough and Johnny arrive at what is supposedly the Tower of London (where the Jewels were stolen from). They actually drive up to the entrance of King's College London on Chancery Lane. Even if they couldn't get permission to film at the real Tower, why pick such a well known building as a replacement?
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.
Factual error: Sauvage's headquarters are supposed to be in the City of London, but in one shot scanning from the top to the bottom of the building, a road sign saying "Canada Square" is visible. This is on Canary Wharf, in the Docklands.
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".
Continuity mistake: When the foreign secretary smacks Johnny English in the face after he poured his glass of champagne over her at Sauvage's reception, you can see a Chinese man and a woman standing by the door looking at the incident, but in the next scene when Lorna catches Johnny, the Chinese man is seen talking to the woman next to him.
Continuity mistake: When Pascal Savage is examining his family tree on the table, the tree can be seen when he tries the hat on. Then the scene cuts to the Archbishop. After this when the scene cuts back to Pascal Savage the family tree sheet is nowhere to be seen. (00:29:45)
Revealing mistake: When Lorna knocks out the two guards with the fire extinguisher in Sauvage's office, you can see the extinguisher actually misses the bald guard's head.
Other mistake: When Johnny asks about the tattoo on the archbishop's butt, the subtitles say "Do you or do you you [sic] not have tattooed on your bottom 'Jesus is coming, look busy'?".
Plot hole: At the end of the film, Trevor McDonald reads the news and says "the spy, who we cannot name for legal reasons..." Yet on screen, one of the newspapers that flashes up (I think it's The Times), has a headline congratulating Johnny English by name. He's not going to be a secret spy for long if they reveal that.
Factual error: All monarchs of England are crowned in Westminster Abbey; nearly every monarch since Edward II has been crowned while sitting on the coronation chair with a large stone known as the Stone of Scone (or Stone of Destiny) resting beneath it. This stone was stolen from the Scots in 1496 and given back to them 500 years later, in 1996, but will presumably be loaned back to the English for future coronations. The building in which Sauvage's coronation was being held was not Westminster Abbey, the throne he was sitting in was not the coronation chair, and the Stone of Destiny was not resting under the chair. Trivial points, perhaps, but factual errors all the same. They could have least have made them look the same.
Visible crew/equipment: Before Johnny parks his Aston when arriving in the South of France with Lorna, a crew member in a white T-shirt can be seen reflected in the car door.
Continuity mistake: When English and Bough are discussing their plan to break into Sauvage's headquarters in the plane, the red cut-away handle for English's parachute is on the right side of his chest, but when English lands on the roof of the building, the handle is now on the left side.
Continuity mistake: When the congregation gasp in horror at seeing the Archbishop of Canterbury's bottom at Sauvage's Coronation, you can see in a wide shot of the congregation a woman wearing a white hat and she is putting her hand to her mouth. When we see a close-up of the woman in the next shot, she puts her hand to her mouth for a second time.
Continuity mistake: When Johnny is in the hospital, a doctor comes out of his office and is joined by two nurses who stand behind him, but in the next shot the nurses are now in front of the doctor.
Continuity mistake: When Johnny meets Lorna in the Tower of London for the first time, we see a close up of Johnny's face and Lorna can be seen taking a sip of her champagne. In the next scene, the glass is away from her mouth and she is taking a sip of her champagne for a second time.