The same events in other peoples stories happen differently in terms of what is said by each character, also the fights are different (ie. Sonic and Tails both fight Knuckles, but Knuckles only fights Sonic).
When E-102 is in the Hot Shelter and boards the train, he does so on the left track. After the transition to the next part of the level, he is on the right track.
In Knuckles story, Knuckles spots Gamma on Angel Island and follows him to the Mystic Ruins base to hijack the Egg Carrier before it takes off. But in Gamma's story, Gamma doesn't go to Angel Island until after the Egg Carrier has crashed and Knuckles has already boarded it.
While playing as Sonic in the Sky Deck after destroying the Giant canons, Sonic is teleported to a completely different area with no explanation or possible way he could have got there. This happens several times throughout the level.
In Gamma's story, he finds Froggy alone at Emerald Coast and takes him, but in Big's story, Gamma snatches Froggy right out of Big's hands and runs away.
Start Super Sonic's quest, then immediately after the cut scene, go back to the main menu and select Knuckles. As Knuckles, go to Angel Island, and you will see another Knuckles and Eggman laying on the ground. (This works with the other characters, but is more interesting playing as Knuckles because you can see two of him.)
In Super Sonic's story before Sonic transforms, Civilians can be heard cheering. However no one can be seen in the area or the surrounding building except Chaos, Tikal and Sonic's friends.
Amy's hands regularly clip through her dress.
Before some cutscenes start while the screen is black, you can hear the character models hit the ground when they are spawned in for the cutscene. Some cutscenes even show the characters falling from the sky when they are spawned in for the cutscenes.
If you pause the game during the Egg Carrier transformation cutscene, the Egg Carrier will despawn at the pause menu. It respawns when you resume the cutscene.
Characters Big the Cat and E-102 Gamma are listed as the 5th and 6th characters on the roster of playable characters to choose from. If unlocking all the characters by only playing Sonic's story, E-102 Gamma is encountered/unlocked before Big, and Sonic doesn't meet Big until the battle against Chaos 6 after clearing both Sky Deck and the battle against E-102 Gamma (whom becomes playable after the first encounter in any character's story).
After setting the two up to fight, Eggman comments that Gamma isn't as advanced as Beta is. Gamma was built after Beta and is a later model robot, so it makes no sense why the newest version of a Robot is less advanced then one several models before it.
After Sonic and Tails land on the Egg Carrier, Tails reminds Sonic that they need to find Amy Rose. However, Sonic never told Tails about the incident the former witnessed while at Station Square before taking the train to the Mystic Ruins while the latter whom was still in the Mystic Ruins didn't see Amy while she was captured by Zero being brought into the Egg Carrier.
The end of Tails's story shows footage of Angel Island falling into the ocean; but this incident occurs during the beginning of Knuckles's story - even before he meets up with Sonic and/or Tails.
Sonic and Tails both enter Speed Highway via the skyscraper and enter either elevator. In Sonic's story, he picks up a staff ID card to open the garage door to gain access to it; but in Tails's story, Eggman creates a hole in the garage door using a missile.
The Mystic Ruins Temple and Shrine of the Master Emerald are based upon what the Mystic Ruins and its areas appeared 4,000 years ago prior to the Perfect Chaos incident, and are technically the characters' dreams before waking up. If Tails picks up the Rhythm Badge level-up item from there, he should wake up without it as it shouldn't be possible to retain items picked up in dreams; the Rhythm Badge should only need to be obtained and retained in the present-day/reality like other level-up items do.
In the game's promotional artworks, Big the Cat is shown carrying the Fishing Rod in his right hand. In the game, he carries it in his left hand instead.