Upon the release of Sonic Chronicles: The Dark Brotherhood, Ken Penders, a former writer on the Archie Comics Sonic comics, sued Sega and EA for supposedly using Sonic character concepts he had independently trademarked prior - particularly the Nocturnas Clan, a futuristic echidna tribe which he deemed as too similar to his own Dark Legion, a futuristic echidna technocracy. This lawsuit came months after Archie Comics filed their own suit against Penders due to a breach of contract after the trademarking, causing Archie to allow their contract with Sega to expire so they could negotiate new terms for the rights to create Sonic comics. This legal fiasco ended in Archie settling the case with Penders, losing the exclusivity to produce Sonic comics after negotiations with Sega, and causing them to write the "Super Genesis Wave", a super-charged energy blast utilizing the Chaos Emeralds that acted as a massive continuity rewrite where over 500 original characters and concepts created by Penders and other writers for the Archie Sonic comics were retconned. The Sega case on the other hand ended in a stalemate due to the statute of limitations, and will not be able to continue unless Sega uses characters from The Dark Brotherhood again.

In Chapter 5: Battle for Angel Island, near the bottom left corner of Metropolis overground, there is a Sega Genesis model 2 with a controller, near an EggRobo.

While the game was in development, SEGA of Europe ran a competition called "Sonic Chronicles: A Race To Name" to allow the fans to name one of the groups of enemies in the game. The winner was SEGA fan-site, Sega Nerds' suggestion of "The Zoah," a reference to the town in Panzer Dragoon Saga.