One of the music tracks in the Game Boy Advance version of The Hobbit, "The Magic Music Box" is plagiarized from "Singing Mountain", an unused song from Chrono Trigger that was initially released on the game's 1995 soundtrack album, and would eventually be added into the DS version of the game.

In the DS version, it's possible to defeat the special boss Spoiler:the Dream Devourer found in Darkness at the End of Time by healing. The boss has 32000 HP; the game's HP value is a 16-signed integer (it cannot be higher than 16 bits, and one of those bits only indicates the sign of the number it represents). By using powerful magic that the boss absorbs during its second phase, it can be temporarily healed past 32767 HP (the maximum HP limit for all characters in the game), which overflows the HP counter and turns the boss's HP into a negative number. Since the boss has less than 0 HP, it will be considered "dead" and the battle will end.

In the FMV of the PlayStation and DS releases, Robo is the only playable character without a special ending.

Magazine advertisements and the website for the 2008 re-release of Chrono Trigger on the Nintendo DS used the iconic line "Good morning, Crono!" from the beginning of the game to promote it. However, because the DS version of the game uses a new translation, this line doesn't actually appear in this version, instead being replaced by the line "Crono, are you still sleeping?"