During a cutscene where Sonic, Tails and Knuckles walk through a ruined hallway in the future, Knuckles' model can be seen collapsing into a ragdoll slightly off screen.

The manual states under Tails' and E-123 Omega's character bios that you can use their Fly/Hover abilities until the gauge runs out. However, in the final game there is no such gauge visible on screen.

During the final cutscene of the game, Spoiler:Sonic rushes past Elise, which then causes her to look around. After not seeing anything, one of the girls behind her asks "Miss Elise?". Although Elise replies "It felt like... someone was calling me," the subtitles accidentally include an extra "like" in the sentence.

The English voice actress "Veronica Taylor" was intended to do the voice of "Princess Elise the Third", she even recorded all her lines for the game, but for unknown reasons, she was replaced by "Lacey Chabert." Even in an interview with GameSpy, they ask her:

GameSpy: Did the people at Sega tell you why they wanted you for this role?

Lacey Chabert: They just told me that they thought my voice was appropriate for the character.

In the cutscene "Rouge returns to the present", Rouge receives a message from a soldier at GUN HQ with the line "Report your status immediately. Have you retrieved the Scepter of Darkness?". While the subtitle is correct, the voiceover actually refers to it as the "Book of Darkness".

In the original teaser trailer for the game, Sonic was shown to be able to transform into Super Sonic at will and not just during a boss fight. This was a feature that couldn't be done in previous 3D Sonic games , but was cut during development due to extreme time constraints. However, by hacking the game, an unused gem called the rainbow gem can be found and equipped. When used Sonic performs an animation where he is supposed to transform, but immediately drops to the ground once the animation is complete, a relic of the Super Sonic transformation feature.

Yuji Naka, former head of Sonic Team, lead programmer on the original Sonic the Hedgehog, and Executive Producer of the 2006 game also titled Sonic the Hedgehog, resigned shortly after it was unveiled at E3 2005.

Each of the supporting characters have unused audio instructing Sonic, Shadow and Silver how to defeat each enemy. One example is Knuckles instructing Sonic on how to defeat an Iblis Golem enemy.

Although Knuckles is normally unable to complete any of the levels, it is possible to complete the Flame Core level with him by exploiting glitches in the game. Doing this reveals that he has a fully functional level completion animation and rank-specific voice overs, indicating that he may have had a larger role at some point in development.

Despite going through the same parts of Flame Core at the same time, Sonic and Shadow are not playable in each other's episodes. However, there are unused sound files that suggest that they were going to team up, with Shadow driving a vehicle while Sonic takes out enemies.

The word Iblis, which is used as the name for one of the game's bosses, is an Arabic word (بليس: Iblees) which translates as 'devil'.

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.