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).