Actor Allusion: When Milo first meets Commander Rourke, the latter comments that he "prefers a good western." This could be seen as a reference to James Garner's earlier television series Maverick, where he played a gambler in The Wild West.
Creator Killer: The film's failure at the box office stalled the careers of directors Kirk Wise and Gary Trousdale (who'd previously directed Beauty and the Beast and The Hunchback of Notre Dame); Trousdale has since gone on to work on DreamWorks animated shorts while Wise eventually moved to a few documentaries, but was credited on an animated film with Open Season. In addition, this was the first in the set of dominoes that made Disney give up on traditional animation for abriefperiod. Then they returned to traditional animation for a shorttime, but now it seems as though that won't happen again.
Development Gag: The commentary tells a story about how there used to be a mystic named Zoltan (who used to speak in the third person, for some reason) along for the ride. At one point everybody sounds off after falling down a hole. For the longest time he was still there shouting "Zoltan is okay!" even after his character had been written out of the script. Interestingly enough, Cookie's robotic mule◊ can still be seen in the final film, while Rourke is accused of plotting to sell the Heart of Atlantis to Kaiser Wilhelm, which was a discarded plotline.
Executive Meddling: The film was originally intended to be a creature feature adventure film. Then the Disney execs decided that they needed to get to Atlantis quicker, and so much potential was wasted. Kida was also downgraded into a Faux Action Girl due to this.
Recycled: The Series: A cartoon series called Team Atlantis was planned, but never came to fruition; the Direct-to-Video "sequel" is really just a few episodes of it strung together. Amongst the ideas proposed for this series was a crossover with Gargoyles, which is broadly considered a canonical part of Gargoyles according to Word of God.
Stillborn Franchise: This film's failure to perform led to the in-development sequel getting cancelled and the planned TV series getting recut into a Direct-to-Video film, and also shelved the intended Gargoyles crossover.
A crossover with Gargoyles was planned, but never made. Disney had been planning to make a series out of the movie, but turned it into a direct-to-video when it underperformed at the box office. This is also true with the future of this film's merchandise: To date, the only characters from the film that still appear in the merchandise are, due to Disney's merchandising policy of marketing the villains of flopped pictures, Rourke and Helga.
The submarine ride at Disneyland was originally going to be based off this film, but the film's failure resulted in that ride being based off Finding Nemo instead. However, there is a restaurant at Castaway Cay called Cookie's BBQ, and part of Port Discovery's background music at Tokyo Disney Sea is taken from this movie.
Jim Hill has an article that goes on in length about things that were cut from the movie, which includes deleted scenes of the Squid Bats and Lava Whales. There was also a plan, very early in production, for a magician character, Zoltan the Magnificent.
A behind-the-scenes footage found on the DVD release and one of the tie-in games shows the original intro was of a group of vikings searching for Atlantis only to be attacked by a sea monster while engulfed in a storm, fully animated, voiced and with sound effects. While mystifying, the executives felt no connection nor desire to learn more about the city or its inhabitants so the intro was done over.
According to the commentary on DVD and Blu-ray, during previous drafts, Mole was just a stuffy scientist, Helga and Rourke were going to have a thing for each other, Rourke was going to be a German spy, and the eye over the pyramid on the back of the US dollar was going to be used to help locate the heart of Atlantis. Also, Milo was going to be related to Blackbeard at one point.
According to Word of God on the DVD commentary, each tunnel would have led to a different monster, although we only see one in the finished film.