Honey the Cat is based on Honey (AKA Candy) from the game Fighting Vipers. She was planned for the original arcade release of the game, but was eventually scrapped. However, she was later reinserted into the HD remake of the game.

Dr. Robotnik's name is misspelled in the intro as "Dr. Robotonic".

There are a few unused songs found within the game's data. One is an alternate version of the character select screen (which is used in the options menu in the Sonic Gems Collection port), one is called "Sunset Town" on the official OST yet doesn't make an appearance in the actual game, another is unused and is not found in the OST so it is impossible to tell what it may have been used for, and the final track is named "Hurry Up". Based on the name it sounds like it could have been used for the Death Egg Hanger, but this track goes unused anyway. Strangely enough, this song became the pre-race cinematic music in the Death Egg DLC for Sonic & All-Stars Racing Transformed.

The January 2024 IDW Sonic the Hedgehog comic mini series based on Fang the Hunter revolves around him, Bean the Dynamite and Bark the Polar Bear searching for the mysterious “eighth” Chaos Emerald. This is a reference to the 1996 arcade game Sonic the Fighters (Bean and Bark’s debut game), which erroneously featured eight Chaos Emeralds, each one owned by the eight playable characters.

Sonic and Dr. Eggman’s cameos in the 2012 film "Wreck-It Ralph" and its 2018 sequel "Ralph Breaks the Internet" can be attributed to an arcade cabinet for Sonic Championship (the international title used for Sonic the Fighters outside of Japan) being in Litwak’s Arcade. Despite the game using the classic designs for the characters, Sonic and Eggman are shown in their modern designs inside the gaming world.

All the playable characters were originally intended to have heartstruck expressions where they blush with hearts in their eyes, but only Bean's expression is used in the final game as a rare random object which Amy can drop using the special move "Heads Up!"

Normally Dr. Eggman only fights while in one of his mechs, but he can be playable in mechless form through hacking.