My version of Pokemon Colosseum (US version, purchased back around the time of release) contains one disc. The disc is mostly black, with red text for the "Colosseum" name and for silhouettes of Umbreon (left) and Espeon (right). The cover of the case contains the Johto dog/whatever you want to call them trio at the bottom, the "Pokemon Colosseum" text in the middle, Groudon and Kyogre near the top, and a translucent version of the protagonist's face and chest near the very top of the box.
The "extra disc" version could refer to the Jirachi bonus disc, which came with some versions of the game. Those ones may come with different box art that mentions the bonus disc. The disc, as the name suggests, is a nice bonus, but is in no way necessary to play the game, and has nothing to do with the game itself (I think it just gives you a special Jirachi for your GBA games). The version I have (described above) is the complete game, if that's all that you're looking for.
