Character mistake: When Johnny English is dismissed from the MI7, Pegasus incorrectly states that he insulted the Foreign Secretary at Sauvage's party. In reality, he sexually assaulted her, spilling wine over her and fainting onto her breasts, but he didn't say anything besides mumbling "Foreign Secretary." The line could be referring to a deleted scene, in which he actually DOES insult her, but this scene took place at Agent One's funeral and not Sauvage's party.
Continuity mistake: During the opening sequence, Johnny English's gun initially has a trigger when it is placed on the table. In the next shot, when Johnny is posing with the gun, the trigger has already disappeared, before the scene that depicts him re-assembling the gun, which is where the trigger is implied to have disappeared.
Chosen answer: The pen is equiped with tiny tranquilizer darts. That's what hits the secretary. The tranquilizer seems to have either a very long effect or some side effects, as the secretary is partly immobilized thus the wheel chair.
Christoph Galuschka ★