In the Sushi Bar scene, when Johnny English and Agent Lorna were toasting, Johnny said a sentence in Japanese which subtitled into English as "May all your daughters be born with three bottoms". What he actually said in Japanese was "Kimi no musumesan-tachi ni chiisai chinchin ga tsuitemasu you ni", which literally means "May all your daughters have small penises".
The Johnny English character is based on a cowardly, incompetent spy played by Rowan Atkinson who first appeared in a series of television commercials for Barclaycard, with his assistant Bough (then played by Henry Naylor). The "poison dart pen" sequence is based on a scene in the commercials where Johnny shoots himself in the leg with the pen.
At one point, English mentions a singing technique to find his way through a darkness, which he states has to be in E-flat. Although the first note he sings is a B-flat, he is actually singing in the key of E-flat.
The Chinese title of this film literally translates into "Mr. Bean (or 'silly bean' as he's called in Chinese) Becomes a Secret Agent". In Brazilian Portuguese it's "Mr. Bean - Um Agente Muito Louco" (a very crazy agent).
There is a scene in which Rowan Atkinson plays the part of Baron De Witt, a crazy man who was in line for the throne of England ahead of Pascal Savauge, however this scene was cut from the movie. It can be viewed in the deleted scenes on the DVD Special Features menu.