When the turtles are eating pizza, Alfred asks if they want napkins. The turtles ask "What for?" This is a reference to Teenage Mutant Ninja Turtles 2: The Secret of the Ooze, where April asks the turtles if they want napkins and they respond in the same way.
Previously Batman and the Ninja Turtles appeared together in three comic book crossovers that were published jointly by both DC Comics and IDW Publishing (the Ninja Turtles' comic book publisher as of release); the first one published by DC serves as the source material for the film. They also appeared together in the video game Injustice 2 (2017).
When The Shredder first fights Batman, he jumps down from a high platform and lands on his feet in slow motion in the exact same way he did during the final fight in the Teenage Mutant Ninja Turtles (1990) movie.
It is the first fully-animated TMNT film to be rated PG-13. It is also the first Nickelodeon animated film to be rated PG-13.
Baxter Stockman's voice is an homage to Jeff Goldblum in The Fly. (1986)