One of the pre-order bonuses for the game is a skin for Shadow that is based off an early concept version of him from Sonic Adventure 2 named Terios. The name comes from the Greek term "telos", referring to an end, fulfillment, completion, goal or aim.

Sonic X Shadow Generations' title was leaked a day prior to its reveal by notable leakers and a URL registration. Following the leaks, some fans and gaming news websites jokingly noted that the term "Sonic X Shadow" had previously also been used on the internet since the 2000s to refer to fan art, fan-fiction and slash fiction depicting the hedgehogs as a romantic couple.

After defeating the final boss, Modern Tails & Classic Tails are briefly seen discussing something at Sonic's birthday party during the game's last cutscene. What they are talking about differs between the English and Japanese localizations of the original game.

In the English version, they said:
Classic Tails: He collects how many? Wow, where does somebody put all those gold rings?
Modern Tails: You know what? I don't know. I keep forgetting to ask.

In the Japanese version, they said:
Classic Tails: You added legs to the plane? What have you done to Sonic's Tornado?
Modern Tails: Yeah... I guess really did go overboard with the legs...

In Sonic X Shadow Generations, the English version of this cutscene was completely re-recorded by the original voice cast, where they now say:
Classic Tails: So I have a question for you. Once we're home, you think the timeline will be restored?
Modern Tails: Yep! Just... don't think about it too hard.

After finishing Green Hill Zone as modern Sonic in the original game, Sonic will mention to Tails that the area seems awfully familiar, with Tails saying "not to me." Green Hill Zone was from Sonic 1, while Tails didn't come into the series until Sonic 2, meaning Tails would have no memory of the area. In Sonic X Shadow Generations, this cutscene was completely re-recorded by the original voice cast to removed this reference by having both Sonic and Tails be familiar with Green Hill Zone and mentioning South Island, the main setting of Sonic 1.

According to producer Shun Nakamura, the events of the DLC stage "Tokyo" (which sees Shadow being briefly sent to the reality of Paramount's "Sonic the Hedgehog" film series and inhabiting his counterpart's body) are meant to be treated as bonus content rather than being part of the game's main story or tied directly into the film series.

After finishing the Chaos Island acts, one of the things Big the Cat will say to Shadow when talking to him in the overworld is that he had been on the ARK and that Shadow passed by him a few times while searching for Froggy, referencing the many cameos that he had in Sonic Adventure 2.

After rescuing Knuckles in the original Sonic Generations, he asked Classic Sonic if he had suddenly gained weight, leading him to insecurely rub his belly. In Sonic X Shadow Generations, this scene was rewritten and re-recorded to instead have Knuckles ask if he knew where the rest of Angel Island is. However, the original animation where Classic Sonic rubs his stomach was left intact, appearing to imply that he ate Angel Island.