On page 41 of the instruction booklet is a sentence that mentions an attack called "SELF REVIVE". This attack does not exist in any Pokémon game.
Although both Pokémon are seen on the box, neither Groudon, nor Kyogre can be caught in the game. This is the first, and (so far) only time that a Pokémon that appears on a game's cover is not found in the game.
Pokemon Colosseum contains character models based on Pokemon FireRed and Pokemon LeafGreen, despite these GBA games being released two months after Pokemon Colosseum in Japan. The models can be seen in the game's multiplayer mode if a FireRed or LeafGreen cartridge is registered.
Rui had her shirt and skirt lengthened for the English versions of the game. This was to cover her navel and make her outfit more family friendly.
Spoiler:After you've caught every Shadow Pokémon except one, a trainer appears at Outskirt Stand. His entire team, except his Shadow Togetic, will be made up of the Pokémon that replaced the Cipher Admins' Shadow Pokémon during their rematches. Before the battle begins, he also states "I am you and you are me and we are all together," a line from The Beatles' song "I Am the Walrus".