The European box art for Sonic 3D: Flickies' Island was not a CGI image, but rather a clay model created by Me Company, a Japanese clay studio whose in-house style involved digitizing its models and editing in elements to make them appear computer-generated.

Sonic 3D Blast's original name was Sonic Spindrift. Developer Jon Burton stated that he did not remember why the name was changed, but still liked it.

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 versions of Sonic 3D Blast and Mickey Mania: The Timeless Adventures of Mickey Mouse have a rather unique exception handler. It can be triggered by punching or shaking a Sega Genesis while either game is playing, causing the game to display a 'Congratulations' message about finding a secret level select, before taking you straight to the level select itself. Traveller's Tales founder Jon Burton, whose company developed both games, explained in a YouTube video that it was the result of a loophole made to speed up Sega's tedious quality assurance pipeline by having the level select appear as a failsafe when the game crashes, meaning that Sega testers would simply believe they had unlocked a secret.

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.