In the stampede after the crowd discovers the dinosaurs are real, at the point where Louie says, "Meet you in Central Park, now run," a caricature of Steven Spielberg with an Amblin Entertainment Logo Baseball Cap and Jurassic Park Logo T-Shirt appears briefly on the left hand side as part of the crowd running towards the camera.
To promote the movie's release, a giant helium balloon of Rex the T-Rex was included in the real-life 1993 Macy's Thanksgiving Day Parade in New York. Unfortunately, as the parade moved through Columbus Circle, high winds caught the Rex balloon and caused it to list over the nearby sidewalk. The head of the Rex balloon struck a protruding street light and popped, but the rest of the dinosaur's body remained inflated until the end of the parade. Coincidentally, in the actual movie, there is a scene where Rex accidentally pops a dinosaur balloon in the Macy's Parade.
A scene in which Prof. Screweyes cages and chains the dinosaurs was fully animated, but ultimately cut from the movie on the grounds that it was too intense. Shots of it can still be seen in the original trailer.
Actor John Malkovich was originally set to voice the role of Professor Screweyes but dropped out because of disagreements with directors Phil Nibbelink, Simon Wells, Dick Zondag, and Ralph Zondag's vision of the film. However, Malkovich's voice can still be heard in one of the film's deleted scenes (found on YouTube as of May 2009). Upon the movie's release, Malkovich was a vocal critic of the project, arguing that the scope of the script was not fully realized and that the final product was "sub par, to say the least." To this day, Malkovich generally refuses to talk about the film. In a rare 2003 interview, Malkovich made a brief allusion to the movie, saying, "Good ideas go to die in Hollywood. I worked on an animated movie about dinosaurs in New York once. It was completely bureaucratized. They took something that had art in it and put it in the laps of people that only cared about the bottom line, and look what happened." In a later portion of the interview, Malkovich went on to say, "Yeah, projects like We're Back: A Dinosaur's Story-they just make you sick. That's why I left this town. It's all about the money, the bottom line. It's disgusting." Director Phil Nibbelink has offered an alternative version of the story were Malkovich was let go after Speilberg rejected his performance as too dark and frightening.