The abandoned subway station, which serves as the Turtles' new lair, is based on the real life "City Hall" Station of the former Interborough Rapid Transit company in New York City. Although the station itself is decommissioned, the track on which it is located is still active.
In the original script, the film was to end on a cliffhanger, with Prof. Perry being revealed to be a robotic shell for an utrom, aliens from the original Teenage Mutant Ninja Turtles comics who created the ooze to power their technology. This was dropped due to the fear of kids mistaking it for Krang, a villain of the cartoon series who was based on the utroms.
At one point during the club scene with Vanilla Ice performing, Leif Tilden (the actor in the Donatello suit) was supposed to roll stuntman Dan Pesina (a Foot Soldier) and then do a side kick like choreographed. However, Tilden decided to do a roundhouse kick instead without first telling Pesina, and as a result, Pesina almost had his two front teeth knocked out.
When Vanilla Ice first arrived on the movie set, Michelan Sisti (the actor in the Michaelangelo suit) went up to Vanilla Ice to give him a hug and welcome him aboard on the movie. However, Ice's overweight bodyguard stiff armed him - even with the full Turtle suit on - and nearly eighteen of the actors and stunt men, including Dan Pesina, stepped forward to pounce and defend Sisti. The film's stunt coordinator, Pat E. Johnson, immediately stepped in and stopped them from fighting. Pesina later told the incident in an on-line interview and said that, "[Vanilla Ice's] bodyguards almost got their butt kicked."
When the Turtles first encounter Tokka & Rahzar, Michaelangelo asks, "Didn't we see these guys on WrestleMania?" In fact, Kevin Nash (Super Shredder) would later appear at four WrestleMania events, including defending his World Wrestling Federation Championship at WrestleMania XI.
In the original film, the turtles facial expressions were cable operated with all the motors, servos etc housed in the shell. In this movie, thanks to a larger budget, the animatronics were much smaller and lighter and were built into the face itself.