- Big-Lipped Alligator Moment: In The Bismuth Crystals, there's an intermission where a member of the ensemble cast finds that his schoolbag is frozen in place and pantomimes trying to carry on with it. It has no bearing on the plot and no one talks about it again.
- Broken Base: The fact that a musical even exists for a franchise known for its edgy, dark story has made some fans cringe. You'd be highly forgiven for not even knowing a musical exists because the Western fandom generally has no interest in the stage shows. Another faction of the fanbase feels as Persona 3 has been too overhyped and has become a massive Cash Cow Franchise just like Persona 4 had been. A third faction remains bitter that Persona 3 is getting a lot of media spin-offs like Persona 4, while nothing is being made for the original Persona and Persona 2 games.
- Hilarious in Hindsight: Mitsuru is notorious for using Marin Karin at the most inopportune moments in the original PlayStation 2 releases of the game. In The Blue Awakening, she has a musical number to herself when she gets hit with Marin Karin. In Sakuya's version of The Ultramarne Labyrinth, she's hit with it again.
- Ho Yay: The Ultramarine Labyrinth unintentionally makes it look like Ken has a crush on Shinjiro. At the Summer Festival, while Ken is admiring the booths, Shinjiro walks across the stage just to casually hold his hand so he won't get lost, and Ken can only look at his hand happily and say, "Aragaki-san, your hand is warm." When they watch fireworks, Ken even reaches over and grabs Shinjiro's jacket shyly.
- During his cast introduction, Jin's actor, Yuichi Matsumoto, introduced himself with this: "My name is Yuichi Matsumoto, and I play Jin, who will be by Takaya's side forever."
- Narm: The Chariot and the Justice battle in The Ultramarine Labyrinth starts off ridiculous. Shinjiro protects Ken from an attack and then starts rapping "Deep breath, Deep breath" while everyone else fights the Shadow as if nothing is happening. Then, it suddenly shifts to another choreographed battle that has Akihiko, Fuuka, Mitsuru, and Aigis running in a circle, culminating in Fuuka and Aigis harmonizing "Battle For Everyone's Souls" while everyone else is dancing. It has to be seen to be believed.
- Special Effects Failure: The backgrounds and the battling are projected onto a screen. Some of the effects, such as Fuuka gathering data inside Lucia, look great. Others, such as Ken scaling the walls of Tziah after getting chased by the Reaper, don't look as wonderful.
- Viewer Gender Confusion: Shouta Aoi, who plays Sakuya, is male, but since his voice is naturally soft and high-pitched, it's easy to mistake him for female.
YMMV / Persona 3: The Weird Masquerade