Events in the gameplay which doesn'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.
- 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 or carrying it over from New Game Plus, 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. Downplayed in Royal, where he reveals himself to have survived, with the true ending indicating that this was in fact real and not a result of Maruki's reality-warping like everyone assumes.
- On New Game Plus, if you go into battle against the vanilla Final Boss with Satanael among your Personas, it ultimately ends with Joker turning Arsène into the building-sized Satanael, despite the fact that you already have him with you.
- 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. With Ann for instance, if you max out her 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.
- 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 is strong against 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 implies that they may have been able to ignore his power, however.
- 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 the teammates only consisted of Akechi and Yoshizawa then 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, Haru and Futaba still interact with Akechi otherwise, as they'll play billiards with him, both of them have several conversations with him in Mementos, and Futaba still congratulates him in combat if he does well in the same manner as everyone else.
- By the time you make it to the 7th Dungeon, you know who The Traitor is (Akechi). The 7th Dungeon's "Time is Up" cutscene involves The Traitor invading your hideout. The Traitor is also the last mid-boss of the 7th Dungeon, and once you beat them, circumstances arise (Namely, Akechi pulls a last second Heel–Face Turn and apparently goes down in a Heroic Sacrifice to save your party from an ambush. His confidant even hits 10 right there.) that remove The Traitor from the story. The segregation arises from the time up cutscene not changing whatsoever after this event. Of course, since the spoilered event in question happens just before you reach the Treasure Room, and you can send the Calling Card the very next day, you will most likely have to go out of your way to view this scenario.
