Dummied Out: Farfinkle, one of the viral Chao, cannot be unlocked in the Japanese version of the game. This involves a Game-Breaking Bug with its special ability to inflict a random status effect.
Echidna versions of all the Blue Ridge Zone Sidequest characters, notably Timothy and his Father, less hilariously actually a child named Timmy, along with dialogue to match that fact.
A robot Echidna with an arm cannon (Think Mega Man)
Unused art for items (And possibly the items themselves)
Flip-Flop of God: Kevin Eva, who was the community manager of Sega Europe in the mid-2000s, stated that Sonic Chronicles is non-canon to the main games. However Aaron Webber, who is a social media coordinator at Sega of America stated that "everything is canon".
Franchise Killer: Not the franchise as a whole but this game can be considered an Unwitting Instigator of Doom when it came to what ultimately happened to the the comic. It's overuse of elements from the comics ended up causing a lawsuit from Ken Penders; which not only killed what hopes Sonic Chronicles had for a sequel but also ended up gutting a large part of the comic's cast when Penders left with the rights for the characters after winning the said lawsuit. This disaster caused SEGA to take a more active approach when it came to the comic to prevent a situation like this from happening again, which in turn caused friction between them and Archie which, among other reasons such as financial concerns, caused Archie to ultimately pull the plug on the comic.
Obvious Beta: Hoo boy. Though the music is the most obvious sign that the game was never properly finished, it's far from the only one.
Stillborn Franchise: The game was not well received enough to get work on a sequel going at a Sonic-level speed, and when Penders rose up in 2010 it put the kibosh on the plans for the RPG series.
Screwed by the Lawyers: Since the whole debacle with Penders claiming the Brotherhood characters were copying from his works, it's very unlikely Shade, Ix and the Marauders will ever be seen another Sonic media again.
Vapor Ware: The sequel, Bioware seems to have completely shut down any and all handheld development that isn't part of their Jade Empire series (which also seems to be Vapor Ware after four years of no updates).