Dr. Starline the Platypus from the IDW Sonic the Hedgehog comic series is inspired by a glitch character from Knuckles' Chaotix - a silver, red and charcoal Knuckles recolor, known by fans as "Wechnia", but by the game itself as "**********", seemingly based on unused data for Tails. Starline's color scheme is taken directly from Wechnia, his name is a literal take on the name "**********", (or "star-line") the black streak in his fur resembles the red streaks all over Wechnia's fur, and the choice of a platypus seems to be inspired by how certain Wechnia sprites would make the bottom of his muzzle yellow and loosely resemble shading for the underside of a flat bill, alongside platypi being Australian like echidnas.

Like most of the other Classic Sonic games, Knuckles' Chaotix features multiple endings. While the "bad endings" of other 90s Sonic games tend to simply run off of implication (such as having Dr. Eggman taunt the player while in possession of a given game's powerful MacGuffin), the bad ending of Knuckles' Chaotix opts to directly show the consequences for the player's failure to collect the Chaos Rings, and shows Metal Sonic Kai demolishing a city into flames on-screen.

There's an unused sprite found in the game of a bloody skull with Japanese text the reads "tobu" (とぶ), which means "to fly, to jump". There is no evidence to indicate what it was meant for, it is quite possibly a joke.

Mighty the Armadillo's sprite sheet is nearly identical to Sonic's sprite sheet from Sonic Crackers, a Genesis prototype game from which Knuckles Chaotix drew its elastic ring mechanic.

This has led fans to speculate that Sonic was originally intended to be in the game instead of Mighty, but was changed late in development. This, as well as the theory that Tails was also meant to be included, is backed up by other assets in the game, including Amy Rose being hidden in a sound test and Sonic and Tails appearing in the ending screen when the game is completed with all 7 Chaos Rings.

Knuckles Chaotix is the only Sonic-related game released on the Sega 32X.

Standing still for a minute will cause Metal Sonic to appear and attack.