Even though Pokémon Crystal is incompatible with the Game Boy, Game Boy Pocket, Game Boy Light, Super Game Boy and Super Game Boy 2, there is an unused Super Game Boy border programmed into the game. This can be seen by setting a flag in the game's RAM to enable the Super Game Boy features. Cheating devices such as the Game Genie can also be used to achieve the same effect temporarily. The border is a leftover from the Japanese version of Pokémon Gold; the design is the same and the text reads Pocket Monsters Gold Version, rather than the English version's title of "Pokémon Gold".

When the player attempts to play the game on a model of the Game Boy prior to the Game Boy Color, the error message "This Game Pak is designed only for use on the Game Boy Color." is output by the game, with the word Crystal spelled out using Unown. There is an unused color palette associated with this message, using an orange tint, which appears when triggering the unused Super Game Boy border.