Just before Sonic transforms into Super Sonic near the end of the game, the surviving crowd in Station Square can be heard in the background chanting Sonic's name to encourage him. This crowd recording is actually comprised of over one thousand attendants in the audience for the official reveal of the game at the Tokyo International Forum on August 22, 1998. The chant was led by special guest Hiroshi Fujioka portraying Segata Sanshiro, the Japanese advertising mascot for the Sega Dreamcast's predecessor the Sega Saturn, and recorded by Sega to use in the game.

In Final Egg, two large stasis tubes can be found. One holds Metal Sonic, while the other holds an unknown Sonic-based robot, later referred to as Mecha Sonic Mark III by Ian Flynn. This robot has no importance in the story, however, it seems to be based heavily on the design of Mechagodzilla from the "Godzilla" franchise's Shōwa era, due to many similar parts and possible textures from the robot. This also seems to be a reference to Mecha Sonic Mark I, also known as Silver Sonic from Sonic the Hedgehog 2, whose concept art also shows similarities to Mechagodzilla.

In Speed Highway, several billboards can be found depicting an unknown female character. In 2020, Satoshi Okano, a former designer at Sega who worked on Sonic Adventure, revealed that this was a scrapped spider character he designed with the prototype name "Spider Girl", and posted an old sketch of the character alongside a sketch of another scrapped character, a bat named "Fly the Vampire". In 2023, Okano posted an inked version of the original Spider Girl sketch from the same time period alongside several inked sketches from the development of Samba de Amigo. Spider Girl's appearance on the billboards in Sonic Adventure suggests that the character lasted far enough into the game's development to receive a 3D model, but was ultimately scrapped for unknown reasons, and this 3D model has yet to surface on its own. It's unknown what role either Spider Girl or Fly were intended to have, though fans have noted that Spider Girl has some similarities to Rouge the Bat from Sonic Adventure 2, namely that both characters have large bosoms and prominent heart-based/romantic imagery.

In the 2021 Batman comic Legends of the Dark Knight #4, the front of the abandoned casino which Batman arrives to is based on the level Casinopolis from Sonic Adventure.

In the E3 1999 demo of Sonic Adventure, Knuckles had a very different voice. This was the same voice actor, but they re-recorded nearly all of his lines before the game's release. Surprisingly, voices for his entire story were included, even though the demo only had two stages for Knuckles.

The game's composer, Jun Senoue, initially went through and scrapped 8 different prototype iterations of the game's main theme song before settling on Open Your Heart.

Sonic Adventure had a limited edition release available two months before the release of the SEGA Dreamcast in North America. SEGA signed a deal with the game rental company Hollywood Video that let people rent a SEGA Dreamcast two months before the release of the console with a selection of games, one of those being Sonic Adventure Limited Edition. Although those copies were never meant to make it into the hands of the public, the copies that did make it to the public usually are incomplete or have a Hollywood Video sticker on the top of the disc.

Big the Cat was purposely created to move at a different pace and to break up the fast-paced action seen so far in the game. Fishing was chosen due to the fact that "he is well... a cat.".

The music for Red Mountain is a remix of "Crying World", the theme from Ristar. It also uses samples from Super Cat's "Ghetto Red Hot (Hip Hop Mix)".

Knuckles originally had an uppercut move but it was cut for unknown reasons.

In the HD port of Sonic Adventure DX: Director's Cut, starting Mission 12 as Knuckles reveals several posters from other Sonic games and media:
•Sonic X, the animated series
•Sonic Unleashed
•Sonic the Hedgehog 4
•Sonic the Hedgehog (2006)

During Sky Chase Act 2, Tails pilots the Tornado 2. The life bar, however, still shows the orginal Tornado 1 life bar. What's odd about this is that there is an unused graphic in the game's files that was going to be used for the Tornado 2, but goes entirely unused.

A leftover title screen from the Tokyo Game Show version of the game exists within the game's code.

Some objects were removed the game's original release, but were later discovered in the PC version of the game. The objects include an unused button in Lost World, a tumbleweed object in Windy Valley, a trash can object in Speed Highway, and an icicle object in the Icecap stage.

Six images can be found in the game's data that appear to be part of an old character select screen.

An unused Clock item icon can be found in the game's files. It's possible that it may have functioned the same way as "Chaos Control", or was a way of adding time to E-102 Gamma's levels, as they were all on a strict time limit.

There is an unused spring model that can be found in the game's files. It looks very similar to the springs used in Sonic Jam's Sonic World. Its texture appears to be used for the switches in the final game.

Several unused Tikal voice clips were discovered inside the game's files, including her talking about the Leon badnik, an unknown enemy called "Golah", and a clip referencing that Super Sonic was supposed to be usable in standard levels.

A prototype loading screen exists in the game's data. It was used in the Sonic Adventure '98 AutoDemo.

In the first cutscene of Sonic's story, Eggman is seen standing on top of building with a guard rail in front of him. This guard rail was removed, and the roof texture was changed in the DX version of the game.