When Orbot installs a new voice chip for Cubot, he says "The think bone's connected to the talk bone, the talk bone's connected to the mouth bone...". This is a reference to Dem Bones, a traditional song written by James Weldon Johnson.

In the post credits cutscene, Cubot says "What's up with those things anyway?", whereas the subtitles say, "What's up with those guys anyway?"

The boxart for the North American Wii version of the game includes a spelling mistake on the back of the box, with the word "perform" misspelled in the line "and preform new moves".

In any zone of Aquarium Park, if the player uses a boost to run on water and then activates a Laser Wisp mid-run, they can aim it into the water. If Sonic then hits a breakable block, the game still assumes Sonic is above the water, giving him normal physics while underwater and preventing him from drowning. However, this also prevents him from using any of the Drill Wisps or jumping towards the surface of the water.

If the player attempts to use a Rocket Wisp powerup while touching the underside of a platform, the Wisp will leave Sonic and fly away, staying in-game for 12 seconds. By doing this multiple times and then activating the powerup normally, it's possible to grab the onscreen Wisps to restart the powerup's timer multiple times, allowing the player to move past the stage's boundaries.

Six levels in Game Land share the same structure as the first acts of every zone in the original Sonic the Hedgehog.
Act 1-1: Green Hill Zone
Act 2-1: Marble Zone
Act 3-2: Scrap Brain Zone
Act 4-1: Spring Yard Zone
Act 5-1: Labyrinth Zone
Act 7-1: Star Light Zone

An unused Eggman voice clip found in the Wii version implies that the Wisps' Hyper-go-on energy is more powerful than Chaos energy. But this may not be the case, as Super Sonic is able to beat Nega-Mother Wisp in the DS version.

The cutscenes where Eggman, Orbot and Cubot are sucked into the black hole and then are seen missing in space do not appear in the DS version.

During the final cutscene in Sonic Colors, the player is given a glimpse of Tails' computer. There are three sets of hexadecimal numbers, and Tails translates the first two. The bottom set, when interpreted as Shift-JIS encoded text, translates to the English letters "If you can read this you're a geek!".

In one of Eggman's PA announcements in Asteroid Coaster, he will say, "Would the owner of a yellow car, license plate 1NOM155, please report to the main gate. Your vehicle is in the path of an asteroid, and is about get sma-- Oh, um. Nevermind." This is a reference to Axel, and his taxi, from Crazy Taxi, as his license plate is 1NOM155.

The English script for Sonic Colors, as well as other 3D Sonic localizations up to Sonic Forces, was partially written by Ken Pontac, known for working on children's programming such as LazyTown, Arthur, and Bump in the Night (the latter of which he co-created), and Warran Gaff, best known for his and Pontac's work together on the adult cartoon Happy Tree Friends. Pontac and Graff's renditions of Sonic were significantly more lighthearted than earlier or later 3D games, a highly requested shift at the time that would prove controversial after a few games. This disdain for Pontac and Graff's writing style led Pontac to decline from doing Sonic panels at conventions out of fears that vitriolic Sonic fans will visit and harass him.