During the development of Harry Potter and the Sorcerer's Stone, and Harry Potter and the Chamber of Secrets, EA forbade the developers from including Harry Potter characters that only appeared in the books and not the movies, as Warner Bros. enforced strict policies in an attempt to keep unauthorized on-set footage or photos from leaking. EA was more focused on the home console and Game Boy Advance versions and, as such, they paid very little attention to the Game Boy Color version; EA would be impressed regardless that the developers created a game for a less powerful console than the next-generation ones. Because of this, the Game Boy Color versions of both games were a more faithful adaptation of the original two books. Ironically, Peeves, despite being cut from the first Harry Potter film, appears in the games anyway because Warner Bros. didn't tell EA that he was cut from the movie until the last month of development.

If the player uses the name "FUN" for the top 3 scores for each difficulty in Flitwick Boogaloo, it will unlock a secret side-scrolling space shooter minigame where you play as Harry riding on a broomstick shooting chickens in outer space that shriek like cats when hit. The minigame can be played by looking through the telescope in the Astronomy Tower and pressing Select.