Events in the gameplay which don't mesh with the story and vice-versa in Persona 5.
- When Joker fights a shadow in the In Medias Res prologue (November 19), he only uses Arsene, who has the Eigaon and Brave Blade skills and no others. In the first place, Joker might not have Arsene in his active roster when he gets to that point in the main story, and he almost certainly will have other personas too; in the second place, Arsene does not normally acquire the Eigaon and Brave Blade skills, and he does acquire others. A player can avert part of this trope by giving Arsene those skills through Skill Cards or the Gallows, but at best that downplays this trope.
- During Ryuji's Persona awakening battle, it's possible for him to use lines referring to Joker by said name, even though the group has not established their codenames yet.
- If you make the decision on a Saturday to send Kamoshida's calling card the next day, then the students will be at school, even though they should have Sunday off.
- Interactions with other characters that involves going out to eat and Joker paying for it will not spend any of your in-game money, such as the Gamer Kid's third rank.
- At one point, mob boss Kaneshiro saddles the party with a massive 3,000,000 yen debt, forcing them to change his heart so he calls it off. Through copious grinding in Mementos, it's entirely possible for Joker to actually have the requested amount, but there's no option to actually pay off the debt and the story still acts as though he can't afford it.
- In the sixth Palace, it is possible to grind Tokens to 100,000 without having to access the High Limit floor. When the bridge activation scene plays out, Crow will still give the player his winnings... from bets on activities the player has not done yet.
- For Kawakami's Confidant, she asks you to call her from another phone than your own so that there isn't any record of you using a maid service to hire her on your phone. However, she'll still text you to request you use her service and (in Royal) call your cell directly after meetings to check in on you...leaving a record of you using her services as a maid (the latter case could be explained away if she uses her personal phone, which would just show you getting a call from your teacher. The former case, not so much).
- If you fail the deadline for the Cruise Ship Palace after defeating Black Mask (which requires going out of your way to do so, since it's possible to send the calling card and do the final heist on the same day), he'll show up and arrest you despite his apparent sacrifice.
- Several of the Phantom Thieves' in-battle moves that involve shooting - such as their melee critical hits, backup Follow Ups, Bullet Hail, etc - aren't connected to their ammo packs; they'll still pull off these moves even if one/all of them have no bullets left. However, this can be justified by Rule of Cool and Rule of Fun.
- Star's Rank 3 ability, Uchikomi - allowing Follow-Up attacks by backup members - works even if the party member in question hasn't unlocked Follow-Up in their Confidant yet, or even unlocked their Confidant period.
- There are multiple instances where you can be dating someone but the story doesn't properly reflect it. For example:
- If you max out Ann's confidant as early as possible and start dating her before the Hotpot event, she will still tell Sojiro that she isn't dating anyone currently, and later in Hawaii, she and Ryuji will ask Joker what kind of girl he's interested in, with no changes from if Joker and Ann are just friends.
- Relatedly if you max out Makoto's Confidant and choose the romantic route even before the Futaba arc, she will tell Sojiro that she is just friends with the Joker, the night the second latter catches them both in his house.
- When Kasumi (actually Sumire) confesses her love to Joker, if Joker is already dating someone else, there's no way to bring that up. Joker's dialogue options are to either to tell Sumire he loves her too and start dating her, or to tell her he'd rather just be friends with her, even though "I'm already seeing someone" would be the most natural response for most monogamous people.
- In the epilogue, you can give the probation diary, which Joker wrote in whenever you saved, back to Sojiro just before leaving Leblanc to say goodbye to your Confidants. Even after you do this though, you can still save.
- Akechi possesses the same Wild Card ability as Joker, including the ability to use more than one Persona; however, he is not able to switch between them during battle. The game explains that Akechi's lack of bonds with others and inability to access the Velvet Room means he doesn't have any Personas apart from Robin Hood and Loki (who, according to Futaba in Royal, are born of his lies and his hate respectively). Additionally, he doesn't reveal he has Loki until after he betrays the Phantom Thieves. However, it is not explained why he can't switch between Robin Hood and Loki when he rejoins the party in the third semester. The game essentially treats Robin Hood and Loki as Akechi's initial and Ultimate Persona respectively, and like the other party members, unlocking his third-tier Persona Hereward makes him unable to access either. Given that this Akechi is in some way affected by Maruki's actualization rather than being wholly himself, it's uncertain whether this discrepancy is due to Maruki's incomplete knowledge, was intentional on Akechi or Maruki's part, or due to some other conclusion.
- Loki has entirely different stats and skills in his playable form in Royal than he does in his original boss fight, which remained unchanged. Namely, Akechi resists Bless in his boss fight, whereas it's his weakness when he's playable.
- In the beginning of Royal's third semester, Maruki overwrites the cognition of essentially everyone in Tokyo and grants them all their wishes. It takes a lot of work for Joker to make his teammates snap out of this fake reality. However, you will still be able to do the social links of every non-team Confidant. This is possible although they should all just feel the same fake happiness as everyone else in Tokyo does (and thus shouldn't feel the need for your help anymore), and it is never shown that they snapped out of it on their own behalf. The fact that they were able to see the rise of Mementos a week earlier could imply that they may have been able to ignore his power, though that still wouldn't explain why the Phantom Thieves couldn't ignore it.
- It takes a lot of luck, but if the player has Futaba's Treasure Reboot unlocked and the player has stolen anything in the third semester Palace when they only have Akechi and Kasumi as teammates and enters battle, there is still a chance for the skill to activate afterwards, with Futaba still announcing it.
- Joker and Maruki's fistfight looks exactly how a fistfight between a counselor and a high school student would look like without Personas... except that at this point, Joker should have enough combat experience to be a proficient combatant even without the use of any powers. Though this is after the entire Final Boss battle(s), so it's likely Joker wasn't at his peak regardless, and he doesn't want to seriously hurt Maruki; just enough to let him vent his inner turmoil.
- Akechi's stats and abilities during his boss fight are inexplicably unaffected by his level and equipment from when he was with the party.
- Though they can't play Tycoon with him, and distance themselves from him for personal reasons, Haru and Futaba still interact with Akechi otherwise, as they'll play billiards with the rest of the team (though they will still keep their distance from him), both of them have several (somewhat) friendly conversations with him in Mementos, and Futaba still congratulates him in combat if he does well in the same manner as everyone else, despite being uncomfortable with him on the team.
- Party talks during Palace exploration are unaffected by what those party members currently canonically know or don't know. For example, in Royal it's possible for Yusuke to be the one to draw your attention to Madarame's first Will Seed, calling it by name, but then after claiming it, a cutscene plays where the concept is explained to him.
- The victory celebration after the Kaneshiro arc takes place at the sushi bar in Ginza on July 24th, and there Yusuke will say "...this is delicious. I've never experienced anything quite like it before" even if he has already eaten at the sushi bar in Ginza for the Emperor Rank 7 Confidant event.
- Joker cannot obtain personas from any of the palace minibosses, but there's no in-story explanation for why they are different from other shadows in this regard. What makes it even weirder is that most the minibosses are merely variations of regular personas Joker can acquire (and might have already acquired by the time he faces the boss).
- In the Temperance Rank 10 Platonic confidant, Kawakami will apologize for being late because "A student asked me for some advice as I was leaving." Presumably both she and the student were at Shujin, but it's possible to unlock Temperance Rank 10 on a day when there is no school. Also, when it's late enough to call Kawakami, it's too late for the protagonist (or presumably any other student) to be at Shujin.
