Originally, The End was supposed to have a boss battle in the same fashion as the other Titans from the main story, but it was changed into a shoot-'em-up style battle due to the approaching deadline during development. It is possible however that the revamped boss battle against The End in The Final Horizons DLC Expansion was meant to revisit the original plan, as it more closely resembles the Titan boss fights than The End's fight in the base game.

Originally, Kronos Island, Rhea Island and Ouranos Island were all connected together into one giant landmass, but according to director Morio Kishimoto, the islands were split in response to feedback from playtesters who thought having one big island was not very interesting.

Despite being synonymous with the "edgy" 2000s era of the Sonic franchise that Sonic Frontiers hearkens back to, Shadow the Hedgehog is completely absent from the game. No official comment has been expressed on why Shadow is omitted, however, a month before Frontiers' launch, the game's writer Ian Flynn would quote retweet a screenshot of an interview with writers for the Sonic Boom cartoon claiming that Sega are restrictive on Shadow's portrayal to the point where it's preferable to omit him in spite of his fan-favorite status than work with Sega's restrictions, with the caption "[quote-retweeted] without comment".

Sonic Origins contains leftover data from the then-unreleased Sonic Frontiers. This is how it was first discovered that Big the Cat and his fishing minigame would return in Frontiers.

Once you defeat Spoiler:the Supreme Titan on Easy and Normal difficulties, the game's final boss Spoiler:"The End" will end up being defeated automatically in the final cutscene. However if you defeat Spoiler:the Supreme Titan on Hard difficulty, you will actually have a boss fight with Spoiler:The End before it's defeated in the cutscene.

Both endings are essentially the same except for said boss fight, and the ending song either being "Vandalize" by ONE OK ROCK on Easy or Normal, or "One Way Dream" by Nathan Sharp on Hard.

In rare instances throughout the game, characters that didn't appear in Sonic Frontiers are referenced in passing, such as Cream, Shadow, Rouge, Blaze, Jet, Omega, Yacker the Wisp, and Zavok of the Deadly Six. However two of these voice lines reference Sticks the Badger and Tangle the Lemur, two characters who have not appeared in the mainline game series at all. While Sticks previously had a character page among other mainline characters on the Japanese Sonic Channel website, she has so far only appeared in the spin-off series Sonic Boom, while Tangle has so far only appeared in IDW Publishing's Sonic the Hedgehog comic book series. Thus Sonic's name drop of them in this mainline title essentially establishes the characters as canon to the Sonic game series. This Easter egg came about due to the fact that Sonic Frontiers' writer Ian Flynn is also a co-writer of the IDW comic series, and Flynn later confirmed that he added Sticks' name to the game's script both as a way to introduce her into the mainline Sonic canon, and to test the boundaries of what Sega would let him include in the game. However, he also added that he couldn't promise future appearances of her in mainline games. Flynn had originally planned for Sticks to make her canon debut in the IDW comics: the ending of the "Battle for Angel Island" arc would have revealed that she had been living on the island. This was declined by Sega. As for Tangle, while not directly related to her appearance in Frontiers, Flynn has stated that Sega fully owns the IDW characters, thus making it possible to use them in games.

Spoiler:The beings known as The Ancients that are seen in flashbacks are confirmed by Egg Memo 11 to be closely related to Chaos, the God of Destruction, the main antagonist of Sonic Adventure.

Some of the Cyberspace levels have layouts and elements taken almost directly from previous Sonic games, even if the aesthetics of the Cyberspace levels don't match the legacy ones at all sometimes. They are as follows:

Zone 1-1: Windmill Isle Act 1 from Sonic Unleashed

Zone 1-2: Windmill Isle Act 2 from Sonic Unleashed

Zone 1-4: Green Hill Act 2 from Sonic Generations

Zone 1-5: Chemical Plant Act 2 from Sonic Generations

Zone 1-6: Green Hill Act 1 from Sonic Generations

Zone 1-7: City Escape from Sonic Adventure 2

Zone 2-1: Green Hill Act 2 from Sonic Generations (2D sections)

Zone 2-2: Dragon Road Act 3 from Sonic Unleashed

Zone 2-4: Shadow's Radical Highway level from Sonic Adventure 2

Zone 2-5: Sky Sanctuary Act 2 from Sonic Generations (2D sections)

Zone 2-6: Shadow's Sky Rail level from Sonic Adventure 2

Zone 2-7: Sky Sanctuary Act 1 from Sonic Generations

Zone 3-1: Green Forest from Sonic Adventure 2

Zone 3-2: Savanna Citadel Act 1 from Sonic Unleashed

Zone 3-3: Sky Sanctuary Act 2 from Sonic Generations (3D sections)

Zone 3-6: Rooftop Run Act 2 from Sonic Unleashed

Zone 3-7: Chemical Plant Act 2 from Sonic Generations (2D sections)

Zone 4-1: Metal Harbor from Sonic Adventure 2

Zone 4-6: Chemical Plant Act 1 from Sonic Generations

Development began shortly following the release of Sonic Forces, which drew some criticism for its extremely short length and level design. Hearing this criticism, Sonic Team decided to abandon the development method used since Sonic Unleashed, since they feared the next game wouldn't satisfy fans.

Generally, 3D Sonic games often limited and constrained players from roaming around the scenery, so they decided to make the game completely open-world, with the idea of innovation that hadn't been seen since the original game and Sonic Adventure.