- B-Team Sequel: Tom Cruise asked Brian De Palma to return as director, but he declined.
- Creative Differences: Andrew Lesnie was the film's original cinematographer. He left less than a month into shooting, due to "stylistic differences" with John Woo.
- Doing It for the Art: Because of his huge back-end deals, Tom Cruise was forced to pay for the production overruns out of his own pocket.
- Executive Meddling: Allegedly, John Woo butted heads with Tom Cruise over Woo's cut of the movie. Once editing started, Cruise, under order from Paramount executives, locked Woo out from the offices, again to keep him from protesting the studio's treatment of the film. He suffered almost the exact same treatment earlier with Hard Target.
- Fake Nationality: The South African Hugh Stamp is played by the Australian Richard Roxburgh. His nationality is never explicitly stated in the movie, though, and while Hugh does have an accent, the film is largely set in Australia anyway, and most audiences are unlikely to notice (unless they are South African or Australian, of course).
- Fake Russian: Rade erbedija as Dr. Markovitch.
- Hostility on the Set: Thandie Newton revealed in a 2020 interview with Vulture that she had problems with Tom Cruise during filming of a particular scene set in a balcony, calling her experience a "nightmare".
- Missing Trailer Scene: The theatrical trailer shows three extended scenes which are not in the movie: Ethan saying "Welcome to Australia, mate" to Luther when they first meet, extra line of dialogue by Swanbeck in the ending where he says to Ethan "Well, Mr. Hunt. I don't quite know where to begin," and Ethan charging at Sean and two of them falling off the cliff. Originally, this scene happened right after they crash their bikes and before their fight on the beach. Making-of documentary where stunts from the movie are discussed also shows some behind-the-scenes footage from filming of this scene and couple shots from it; motorbike flying towards camera which is buried in the ground, Ethan and Sean lying on ground after crashing into each other when the other crashed motorbike explodes, and Ethan running towards Sean.
- No Stunt Double: Tom Cruise performed about 95% of his own stunts.
- Another line from Swanbeck from the trailers - "Well, Mr. Hunter, the mother of all nightmares is on the loose".
- Troubled Production: Filming overran significantly which cost Dougray Scott the role of Wolverine in X-Men.
- Uncredited Role:
- Unintentional Period Piece: The rock version of the Leitmotif was done by Limp Bizkit (the song itself plays during the end credits), a band that became Deader Than Disco practically the day after the film's premiere.
- What Could Have Been:
- Oliver Stone was the first director attached to this film in the period after the first film's release. He reportedly wrote a treatment but backed out due to scheduling conflicts resulting from Tom Cruise's prolonged stint on Eyes Wide Shut.
- The part of Mission Commander Swanbeck was originally offered to Ian McKellen. He was not able to accept the role, due to a prior theatre engagement in London, and the part eventually went to Anthony Hopkins.
- The first cut of the film clocked in at three and a half hours. The studio balked at this length and told John Woo that the final length could not exceed two hours. This would explain why there are so many plot holes and continuity errors in the theatrical cut.
- William Goldman wrote a script that wasn't used.
Trivia / Mission: Impossible II