The scene where Colin Farrell's character tells the girl at the bar how he "just got out of jail" was Farrell's idea. He said he used it on a girl in a bar one time and that it worked, so the producers put the scene in the film.
Colin Farrell states on the DVD audio commentary that while filming the scene in which he and Al Pacino's characters go to a restaurant, Al Pacino accidentally damaged the car they were riding in. The resulting damage can be clearly seen in the scene where Clayton and Burke pull up to the restaurant.
At no time in the movie are any Microsoft products shown being used. Several times Macintosh computers are used, and in the scene where James is using Layla's computer while she is in bed, the alternative Opera web browser is prominently displayed, used with permission from Opera Software ASA.
While playing cards with the other recruits, Colin Farrell's character, Clayton, refers to his opponent, a former Miami cop, as "Sonny Crockett". Several years later Farrell would portray Sonny Crockett in Miami Vice (2006).
The glass encased roll of honor that Clayton looks at in his first day as a CIA career trainee includes the names of Deryck Blake, Andrew McAlpine and Dennis Davenport: respectively the Property Master, Production Designer and Art Director on this film.
The CIA questioner asks James a question "Would you rather ride on a train, dance in the rain or feel no pain" which predicts three things that occur to James during the film. His chase of the fugitive (later revealed to be his friend Zack) happens through and under a train, his pursuit of Layla to the train station occurs in the rain and his kidnapping during training where he is tortured, testing his pain limits.
The computer code seen as part of Ice-9 is actually gibberish taken from code written in C for Windows using Hungarian notation for variables and seemingly part of an earlier routine to search for files. It is not syntactically correct - taken as a whole it's just gibberish.
There are numerous references to Kurt Vonnegut Jr., including the computer virus being named Ice-9 (from "Cat's Cradle"), Clayton reading "Slaughterhouse Five" at the coffee shop, and Clayton referring to his father's eggs as the "Breakfast of Champions".
The character of the CIA Career Trainee Lisa Sahadi (played by Elisa Moolecherry) was revealed in a deleted scene to actually have been a CIA agent who is part of the new group and is gathering intelligence on the group.
On the audio commentary of the film, director Roger Donaldson and Colin Farrell joked that the huge rear projection screen on set (valued at $300,000) was powered by turbine pedaling monkeys to make it as bright as it was.
When James Clayton is on his drunken bender in the hotel room he is watching a spoof commercial about preventing sweat stains on your underwear from Comedy Central's The Man Show, starring Adam Carolla and Jimmy Kimmel.