Although his name was changed to Robotnik for the English versions, Dr. Eggman's original Japanese name is still written on the tail fins and bumps on Wing Fortress Zone.

Tails was originally designed as two different Animals before being turned into a fox. First, he was designed to be a flying squirrel. His design was later used for Ray the Squirrel (who would only appear in SegaSonic Arcade). He was than redesigned as a Tanuki, but this idea was scraped since Mario already had a Tanooki suit that made him able to fly.

There was originally a stage called Hidden Palace Zone in the game. It featured an underground cave full of shiny gems. Code for the stage exists on the final version of the cartridge, however it cannot be played through normal means. In an interview, Yuji Naka revealed that the player would be warped to the Hidden Palace Zone when all 7 Chaos Emeralds were collected. There, you would be given the ability to become Super Sonic.

Early versions of the stage can be played in prototypes of the game.