- Complete Monster: Professor Clover, introduced as a mere treasure-hunting burglar, reveals himself to be insatiable greed personified in his second appearance. Kidnapping and posing as a kingdoms general to manipulate the lands princess, he seeks to activate a weapon which would destroy the city, just to get an orb to power up his staff. To gain a rare treasure, Clover murdered the parents of two main characters, leading to both going through horrific childhoods following being orphaned. Previously working as the agent of an unknown federation, Clover again worked to steal another treasure, hoping to use its power to threaten the citizens of the nation containing it to submit to them lest he wipe them from the face of the earth. Manipulative and cruel, Clover corrupts a girl with time-bending powers, using her to steal more treasure and cause more havoc. When the heroes try to save her from his clutches, Clover threatens to murder her with acid, rather than lose her. Clover stands out in a usually-lighthearted series.
- Fridge Logic: They renamed Experiment 101 to Roko, because his name had numbers in it—yet his rename ended up sounding like a number, as well ("roku" meaning six).
- Moe: Hachi is just plain cute. His clumsiness, admiration of Joker and his -"su" suffix only make him more so.
- Tainted by the Preview: When previews of this show surfaced, it caused a stir within the Magic Kaito fandom. It didn't help that Kaitou Joker and Magic Kaito 1412 premiered within two days of each other (see Dueling Shows on the Trivia page).
- Unpopular Popular Character: Shadow Joker is seen as an enemy by Joker and his friends, and later becomes an enemy of Professor Clover and Doubt when he betrays them. While he becomes a reluctant ally of Joker's when necessary, Joker and his friends still seem to dislike Shadow Joker. The only character who truly cares about him is his twin sister Rose. However, in the fandom he is one of the most popular characters.
- Viewer Gender Confusion: President D, and Spade to a lesser degree. This is quickly cleared up upon hearing their voices.
YMMV / Mysterious Joker