The title screen in the North American and Japanese versions are almost completely different, likely due to the game's name originally being Sonic & Tails 2 in Japan. The Japanese version also has an option for "3D Stage" that was removed from other versions.

The box-art for the North American and European versions of the game strangely shows Dr. Robotnik's likeness from Adventures of Sonic the Hedghehog, which isn't seen in game.

One of the game's antagonists Fang the Sniper (called Nack the Weasel in the English release of the game and various English-language comic books) originally wielded a realistic gun in early development screenshots and concept art. However, this was later changed to a cork-shooting popgun during the game's development. According to his character designer Shinichi "Touma" Higashi, Fang was originally supposed to be a gangster-like character with a "slightly futuristic" gun, but as a result of the creation of Knuckles the Echidna around the same time, he was redesigned into a "clumsy, impatient, and somewhat foolish character—someone who was charming and impossible to hate."