In the level Hang Castle, if the Eggman Statue is looked at while upside down, Neo Metal Sonic can be seen. This can only be seen if the player is playing as Team Sonic, Team Dark, or Team Chaotix.
When Team Chaotix's team blast is activated they are supposed to sing, but due to the team blast being too loud, and sound effects cutting it off, it's impossible to hear the singing during normal game play.
The F Rank was supposed to be in the game, but was scrapped for unknown reasons.
After the fight against the Robot Carnival/Storm, Eggman will always say, "Don't get too excited, boys! Those were the easy ones!" regardless of the team being used. This is likely an oversight, as both Team Rose and Team Dark have female characters within them.
Playing as a different character and turning the camera towards Rouge will cause her to turn her head to look at you and wink.
By holding A + Y (or X + Triangle on PS2) after having chosen a team and stage in the 2 Player Mode, the teams chosen will be in their metal states.
In the 2008 edition of the Guinness Book of World Records: Gamer's Edition, Sonic Heroes was featured for having the most playable characters in a platformer game.