A car bears the license plate "Mirage84". The Teenage Mutant Ninja Turtles first appeared in Mirage Comics in 1984.
The mutagen in this film is purple instead of the common green-colored mutagen. This came from Teenage Mutant Ninja Turtles (1987), which featured different varieties of mutagen that formed different mutants.
Brad Garrett, who voices Krang in this film, is best friends with Pat Fraley, who voiced Krang in Teenage Mutant Ninja Turtles (1987). Fraley personally endorsed Garrett as Krang when he was announced.
When Casey Jones is smashing up the bar, "Ice Ice Baby" by Vanilla Ice is heard on the jukebox. Vanilla Ice appeared and performed "Ninja Rap" in Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991).
The Turtles are designed in this film to look more like their Teenage Mutant Ninja Turtles (1987) versions: they look lighter green and wear harnesses (as in the 87 series where they had on belts).