There is an unused multicolored gem in the game's data called the Rainbow Gem. This gem would have let the character "go super" at any time they wanted. If it is hacked back into the game, the character would go through the Super transformations animations, but would be unable to turn into the Super mode.

The game was originally envisioned by SEGA to be a reboot to the entire franchise, and to build the game similar to the Adventure series, fearing that the previous "Sonic Heroes" and "Shadow the Hedgehog" had made the series stray too far. This also explains the realistic art direction that the game took, along with certain character interactions that don't make sense.

In the cutscene where Sonic returns to Soleanna from the future, the newspaper he picks up has the title misspelled as "Daily Soreana"

In Shadow's story, after you ignite the flames around the fountain in Soleanna City and receive the Sceptre Of Darkness, you'll receive a message from GUN HQ that will tell you where you have to go next. The dialogue in the message contains 2 takes from the voice actor, the first take being a failed attempt. It seems that it was accidentally left in the game.

Throughout Sonic's story, there are Gems that gradually become available for purchase from the shops which grant Sonic abilities such as slowing down the environment around him, giving Sonic a burst of speed and even allowing him to throw the Gem in a grappling hook-like fashion. These are supposed to drain his meter in the bottom right-hand side of the screen (which works properly for Shadow and Silver), but due to programming errors, they don't do anything. As such, it is incredibly easy to exploit your way past disliked sections of stages.

Story-wise, this is the only game in the series to feature a villain who succeeds in killing Sonic, albeit soon followed by his revival.

In Sonic 06's manual, there is a section about shields however they cannot be accessed during normal game-play. By modifying the game's code, they can be accessed but can not protect against damage.