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.

If one punches or shakes a Sega Genesis while Sonic 3D Blast is playing, they will access the level select screen. This was not an intentional Easter egg, but rather 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 - this trick had previously been used in the development of Mickey Mania: The Timeless Adventures of Mickey Mouse.

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.