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 2012 re-release of the game as a hidden character. Due to her being an homage to a character from another game, Honey the Cat's appearances throughout the Sonic the Hedgehog series have been limited to rare cameos due to certain rights issues regarding her similarities to the original character, despite both being owned by Sega.

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

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.

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.