What Could Have Been: In one interview, Alan Moore said that he originally considered having Irene Adler lead the team, but ultimately settled on Mina Harker instead because he worried that Adler was too obscure.
At one point Simon Bisley was considered for regular art duties on the book. It boggles the mind...
Director Stephen Norrington had such a bad experience making the film that he announced he would never direct another movie. So far, he hasn't.
Even worse, Sean Connery became so disenchanted with the moviemaking process with this film that afterwards he announced his retirement, except for some voiceover work.
Deleted Role: A character named Eva Draper (Winter Ave Zoli), the daughter of German scientist Karl Draper, was removed during editing but remained in some of the promotional material. Eva had appeared in two scenes: one ended up on the cutting room floor, and she was digitally replaced with a different character in the other. A brief fight scene featuring Tom Sawyer and the replacement character was rotoscoped into the film. The deleted scenes which feature Draper appear on the DVD.
Deleted Scene: A scene was cut from the film where Tom Sawyer explains that he and his friend, Agent Huck Finn, were tracking down the Fantom, and that the Fantom killed Huck. This is the reason why Sawyer is so intent on getting the Fantom.
Disowned Adaptation: Alan Moore, who's already notoriously stingy about adaptations of his work, hated the film so much that he demanded his name be left off of all future ones. It should be noted that Moore was initially okay with the film until legal issues cropped up over the film's similarity to an unproduced screenplay. The fact that the studio settled the lawsuit rather than allow Moore to defend himself ultimately soured him toward any future adaptations of his works.
Executive Meddling: Tom Sawyer was added, because the studio thought many people in the American market wouldn't care about the movie, unless an American character and cast member was in it.
Fan Nickname: Posters abbreviated the title to "LXG," causing certain derisive fans of the comic to call the movie "The League of EXTREME Gentlemen."
No Stunt Double: Naseeruddin Shah trained with a karate master to do much of his own fighting stunt work as Nemo.
Old Shame: Richard Roxburgh later referred to the finished film as "an unadulterated stinker", saying that he realized too late, when he arrived on set during the first day, that the film was going to be a bad experience.
Star-Derailing Role: For everyone; Sean Connery ended his long cinematic career after this movie.
Stillborn Franchise: There were plans for sequels, and the box office had been considerably stronger overseas than in the US, largely due to the presence of Sean Connery, but since Connery had quit films entirely in disgust at how the production had gone along with the director, any heat the franchise had petered out pretty quick.
Troubled Production: As if the conflicts between Sean Connery and Stephen Norrington weren't enough, filming in Prague was delayed when a flood destroyed the set.
Roger Moore was offered a cameo as Campion Bond, a part that was ultimately cut from the script, and would've been the first time two actors to have played James Bond shared the screen.
The ending cuts to Quatermain's hand coming out of the dirt and grabbing his rifle. A Call-Back to what he said earlier in the film, "Africa will never let me die." But that wasn't used because they want to leave it ambiguous. At the least though it left the film open-ended rather then set up for a sequel that'll never come.
Monica Bellucci was originally cast as Mina Harker, but had to drop out due to schedule conflicts.
May not be deliberate, but Moriarty's plot in Sherlock Holmes: A Game of Shadows bears great resemblance to his plot here, as both see Moriarty attempting to trigger the First World War decades in advance and profit by selling weapons to both sides.