In Iron Jungle, if Shadow is accompanied by the Egg Monitor while fighting one of the Big Foot Type A enemies, Dr. Eggman will laugh at it and say "That's just like the Big Foot from Prison Island!" This is a callback to the first boss fights in the Hero and Dark Stories from Sonic Adventure 2, although F-6t Big Foot was fought in Central City, while its more powerful variant B-3x Hot Shot was the one fought on Prison Island.

In Amy Rose's official render for the game, the bottom of her left leg can be seen clipping through the side of her boot.

The text seen in the background of the main menu has poor grammar and many spelling mistakes:

Maria’s card in Sonic Rivals uses an image from a deleted scene in Shadow the Hedgehog where her death is shown in more detail.

The game was originally intended to be more graphic than the final release, with the initial goal being to be given a T Rating by the ESRB. However, part way through the game's development the ESRB introduced the E10+ Rating, so the Development Team decided to aim for that instead, resulting in some of the game's content being censored. This included changing the Black Arms' blood from red to green, editing scenes of GUN Soldiers' deaths, cutting out Maria's death, and censoring some pieces of dialogue.

At Momocon 2024, Shadow's voice actor, Jason Griffith, further revealed that at one point in development, Sega shot for an even higher M rating. According to Griffith, he had to record two takes for every line: one take was the clean version heard in the final game, and the other was an adult-oriented version where Shadow's dialogue was peppered with the word "fuck." Griffith estimated that Sega had "hours of recordings" featuring Shadow swearing at every possible opportunity.

There were plans to have Sonic in the game's multiplayer mode although this idea was cut early on in development. The only thing that remains of him in the game's memory is his Japanese voice clips.

A song created by Magna-Fi, "Who I Am", was originally intended to be used as the game's main theme song. This was later changed to "I Am... All Of Me" by Crush 40.

After completing the "Space Colony ARK Mission", there's a cutscene of "The Eclipse Cannon" destroying the White House along with the city. The way it's presented is a very clear reference to Independence Day.

G.U.N. soldiers will sometimes reference former head of Sonic Team, Yuji Naka, by saying "Mr. Yuji Naka is alright."

After completing the "Hero Mission" in "Westopolis", Sonic will say "Welcome to the next level". This was the original slogan used by SEGA for the Genesis.

According to Takashi Iizuka, the game was created to appeal to the American market.

The game plays out depending on what missions (Hero, Neutral, Dark) are completed per level. In total, despite the game having 10 endings, there are 326 possible “endings” each with their own sequence of levels, cutscenes and unique library entry for each "ark".

This decision made the game notoriously difficult and tedious to 100%. The current segmented world record for a 100% speedrun is over 181 hours long as of September 2021.

Two of the mini bosses in the game, Blue Falcon and Black Bull, take their names from two of the racing machines from F-Zero, driven by Captain Falcon and Black Shadow, respectively. As SEGA helped co-develop F-Zero GX, it's highly likely that these were intentional references to the series.