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.

There is a Debug Mode code accessed from the Sound Test in the options menu that is inputted by playing songs in the order 01, 09, 09, 02, 01, 01, 02, 04. This is a reference to the North American release date of the game, which was on 1992/11/24, or November 24th, 1992.

The code to access the Level Select is 19, 65, 09, 17. These numbers reference Sonic developer Yuji Naka's birthday, September 17th, 1965.

The title screens of Sonic the Hedgehog and Sonic the Hedgehog 2, with Sonic (a character known for his super speed) posing and waving his gloved hand inside of a ring lined with stars and a ribbon banner at the bottom, could possibly be taken from the logo of the 1981 anime adaptation of the Akira Toriyama manga "Dr. Slump" and its speedy protagonist Arale. It should also be noted that the ring surrounding Sonic has giant wings protruding from its sides, which appear to reference the angel wings on Arale's cap that also feature in the intros to the anime and some of the Dr. Slump films.

While it's not known if any Sega employees have commented on this connection, it was acknowledged in the form of a small cameo appearance where Sonic gets outrun by Arale in the 1993 sequel manga "The Brief Return of Dr. Slump".