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.

In the prototype version, Kris had a different design. Her hair was black with pigtails and looks like she may have had different clothes.

In the Dragons Den, you are asked a set of questions by three monks, which result in receiving a Dratini with the move Twister. However, if you give the right answers, you can obtain a Dratini with the moves Twister and Extremespeed.

This was the first Pokemon game to have animated sprites for Pokemon, however it only applied to the front sprites, while back sprites remained still. This was removed again until Pokemon Emerald, after which it became standard.

The Battle Tower originated in Pokemon Crystal and is the only game to allow Legendary Pokemon to be usable, although Mewtwo, Mew, Lugia, Ho-Oh, and Celebi are only allowed if the level chosen is 70 or higher.

This is the last game to include the "Gotta Catch 'Em All" slogan. The rest of the games just include "Pokemon: (Color) version."

There is a glitch where the player's colour scheme can be changed.

This is done through:
1. Starting a game as either a boy or a girl and saving.
2. Starting a new game as the opposite gender.
3. Save the game, but turn it off while it says "SAVING...DO NOT TURN OFF THE POWER".
4. When the player restarts, his or her character should be the wrong color.

You can do this without starting a new game but doing so with Pokemon in your PC will cause them to be lost.

Performing this glitch also unlocks Mystery Gift.

In the Japanese version, the Pokemon Center in Goldenrod City was replaced with a Pokemon Communication Center that allowed players to connect to the internet via use of a cell phone. This system was removed from international versions of the game.