There are unused sets of dialogue in the game which suggest the turtles were supposed to be a lot more chatty.
The Japanese version's name has the subtitle 'Super Turtle Ninja'. None of the other versions have this subtitle.
On the underside of the skateboard Michelangelo is riding on the box art is a Watchmen sticker, a homage to the comic series that came out around the same time.
There are four different types of pizza in the game data: "speedy", "whirly", "sappy", and "energy". Only the energy pizza is used, and restores health. The other three might have been used to give different power-ups, and are color-coded for each of the four turtles. The rom even includes unused sprites of Donatello holding and firing a laser pistol.