In the Dreamcast version of the game, boxes in the Crazy Gadget area have green X's on them. These were changed to red X's for the Gamecube version of the game. It's believed that the change was made because the logo of Microsoft's Xbox is a green X.

A number of Omochao lines were removed from Sonic Adventure 2 but were re-added as an Easter egg in Sonic Adventure 2: Battle for when Sonic or Shadow carries Omochao through the goal ring.

It's possible for Tails to drown in the Hero Chao garden. If he stands in the deep water for 20 seconds or so, a countdown will begin and he will start to drown. This does not deplete the player's lives, and only works with Tails. This does not work in the GameCube installment as the water is not as deep.

The Dreamcast version of Sonic Adventure 2 had official DLC that was available from the game's website. This DLC includes the menu themes that would later be added to the Battle edition of the game, three kart racing tracks with karts exclusive to those tracks (Sonic's special kart, the Eggrobo, and Opa-Opa from Fantasy Zone; the first two are unlockables in the Battle edition), and Halloween and Christmas-themed character skins for two-player mode.

In the final game, Sonic wore SOAP shoes instead of his buckle shoes seen in previous games. However, during development, Sonic was shown to still be wearing his buckle shoes. This can be seen in early screenshots, and the E3 2000 trailer. Remnants of this can be seen in the final game. In the first cutscene of the Hero Story, when Sonic jumps out the helicopter, he is wearing the buckle shoes, but by the end, he is wearing the SOAP shoes. This error was fixed in the GameCube port.

Even though the game has an "E for Everyone" rating, it still has a "Mild Lyrics" warning. This is because both of the songs "Deeper" (theme of Death Chamber) and "Kick the Rock" (theme of Wild Canyon) use the word "damn". Additionally, "Kick the Rock" refers to the character Rouge as "sexy and smooth" followed by an innuendo referencing "jewels" in the next line. The parts in which both songs use the word "damn" are cut out of the loops found in the game, and can only be heard in the soundtrack versions.

The Dreamcast version doesn't contain the warning, as the Mild Lyrics warning was added to the Gamecube version, and is in the rating for every subsequent release.

When the game's logo is shown in the intro of Sonic Adventure 2: Battle, the word "BATTLE" has a shining effect, which is another video file overlaid over the 3D logo. There are two versions of this video, one with Japanese kanji and another with Latin script, however due to an oversight, the shining effect will only show Japanese kanji overlaid upon the English text. This would be fixed in the 2012 rerelease, but only for the English language, so other languages with an English logo still experience the error.