According to programmer Jon Burton, Knuckles' bonus stages were planned to have their own music. However, due to memory constraints, the song couldn't fit onto the cartridge, and Knuckles' bonus stage simply use Tails' bonus stage music in the final game. The song was eventually repurposed in Sonic Adventure as "Pleasure Castle" (Twinkle Park 2).

The Genesis version has a rather unique exception handler. When triggered, the game displays a 'Congratulations' message about finding a secret level select, before taking you straight to the level select itself.

From 1999 up until the release of Sonic Adventure in 2000, Jack in the Box restaurants in the US were selling the PC version of the game either in a kids meals for $1.99, or by itself for $5.99. SEGA was willing to sell the game cheaply as they were expecting to exceed the quality of the game with the release of Sonic Adventure, and thus reduce people's desire to purchase it.

There is an unused music track in the sound test found in certain prototype builds of the game. This track would later be recycled as one of the boss themes for Sonic 4, Episode 1.

The Saturn version was ported in only two months, and was released on the same day as the Genesis version in North America to make up for the cancellation of Sonic X-treme.