After releasing Lyric Sonic says: "He dodged my spin attack, No one's ever done that before." Lyric didn't dodge it, he blocked it with the ball that bound his claws.
In the Eggman boss fight, Sonic and friends destroy eggmans mech to the point where it's unusable and can't move. Eggman escapes in the eggmobile and flies away, however in the final cutscene of the game Eggman somehow gets back inside the mech, and somehow makes it function again, walks it all the way from creeper gorge to lyrics lair, just to shoot lyric once in the back and then the mech collapses again.
At a certain point in a level, Knuckles and Amy would say things like "Good job Perci." Perci is a in-game NPC that offers a side quest in the hub and wasn't even in the area when they say this.
In one scene, Metal Sonic ground pounds causing the characters to fly into the air, when Amy falls her hammer fly's away but when she hits the ground she's holding it again.
In the cut scene where the Chef character is talking, Amy will quip "who burnt the toast?" during this her mouth continues moving after she stops speaking.
During a cut scene, Knuckles punches at nothing but there's still the sounds of a wall crumbling.
None of the ancients ever saw Sonic or Tails in the past so they shouldn't have been able to carve their appearance on the prison door.
At one point in the water purification plant level, Q-N-C appears and Sonic asks "How do you keep following us?" Q-N-C never followed the characters at any point before this.
Lyric says he's going to update Metal Sonic's code to do something unspecified. It's never said what exactly this "update" is and it's never brought up again.