At one point when playing the Grand Metropolis stage as Team Chaotix, Vector will say "Boy, it doesn't look good.", after which Espio responds saying "I'll handle it". The closed captions however instead say "Leave this to me!".

According to designer Shiro Maekawa, there were originally going to be six teams with very different line-ups. Two of the teams, Team Sonic and Team Chaotix, had the same members as they appear in the final game, but the four early teams include:

• Amy, Cream and Rouge
• Chaos, E-102 Gamma and Big
• Fang, Bean and Bark
• Metal Sonic, Ray and Mighty

Due to time constraints and balancing purposes, the number of teams was reduced from six to four, and the members of Team Dark and Team Rose were swapped and adjusted after it was decided that Shadow Spoiler:would not be dead after the events of Sonic Adventure 2.

Pressing the Action/Attack Button and one of the Switch Character buttons on the same frame simultaneously will cause the Flying-type character's controls and animations to glitch out. When this happens, the player will unnaturally accrue 1/3 of their Team Blast meter, meaning that doing the glitch three times will completely fill up the meter, allowing the player to use Team Blast far more frequently than usual.

In numerous levels there are Gongs that Power-type characters must attack in order for their respective team to progress. However, if the player has full Team Blast meter at these Gongs then they can softlock the level or story mode with a glitch. To do this, after using a Power-type attack on the Gong the player must then rapidly switch to the Flying-type character when just getting off the ground, then the player must immediately use their Team Blast. If done right, then the characters will be stuck in an extremely glitched Flying Formation in a black void with no way of getting out, forcing the player to quit the level or turn off the game.

If the player uses an "Infinite Rings" cheat or hack then selects the Casino Park stage in Team Chaotix's story mode, the opening cutscene of Casino Park and the "level finish" cutscene will play at the same time and cause the animations to overlap into a glitchy mess. This is due to the mission of Casino Park being to collect 200 rings, a task that the hack accomplishes upon the level's immediate start-up.

All 12 playable characters have dialogue in the game that goes completely unused. The audio references an object that's referred to as an Omochao-themed gate. This gate would've been opened via the use of a nearby Omochao. However, no such "Omochao Gate" appears anywhere in the game, and Omochao himself does not physically appear in any level of the game either.

A lot of Team Rose's levels end at a much earlier point than Team Sonic and Dark's. However, through the use of glitches, exploits, or cheats, it's possible to go past the goal ring with Team Rose and go to areas that are only accessible to the two other aforementioned teams. The same thing can also be done in some of Team Chaotix's levels as well.

Interestingly, the characters of both Team Rose and Chaotix have fully voiced and functioning dialogue for these normally inaccessible areas.

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 2004, a commercial for Sonic Heroes McDonald's Happy Meal LCD games was aired in Pakistan. This advert would become infamous abroad for the low quality of its CGI animation produced by the company Image Dynamics, with inexpressive and off-model Sonic characters playing sports. In particular, the segment for the game Amy & Rouge Tennis (incorrectly called "Rogue & Amy Tennis" by the narrator) features a version of Rouge the Bat who is unclothed and resembles a mouse, and the segment for Tails Soccer has a one-tailed Tails performing an own-goal.

An English-language re-upload of the commercial to YouTube in 2011 has managed to amass over 8 million views as of 2023, and in 2015 the Sonic the Hedgehog social media pages acknowledged the commercial as being "creepy".

In 2024, footage from more Pakistani McDonald's commercials promoting Sonic LCD games were found online through various portfolio accounts. These ads include an alternate Knuckles model which is simply Sonic's colored red without the dreadlocks implemented, and Big the Cat, who is absent from the better known commercial. Big has two models featured in the portfolios, one that retains his belt and face but gives him white sneakers in place of his sandals, and another that retains his sandals, but lacks his belt and gives him large eyes more closely resembling other anthropomorphic characters in the Sonic cast.

Adding the line "Charmy_Shutup 1" to "%AppData%\SEGA\SONICHEROES\sonic_h.ini" on the PC version will deactivate all non-subtitled speech from the characters during gameplay (including attacks and idle quotes).