These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Logic: Flay is a Senior, and that apparently allows the True Companions to venture the Mana Ruins - Interior Heights. So, why not include the God's Scar and Clocktower into the list?
So Theofratus makes a Mana capable of granting any wishes to atone for his mistake for shortening Jess's lifespan, right? But, WHY THE HELL DID HE USE IT TO KILLS HIMSELF?! Does he ever think that he can use it to fix that mistake? To makes Jess healthy again? And he is supposed to be the most brilliant alchemist ever...
Arguably applies to Vayne as well. Why didn't he think of using his reality-altering power to cure Jess before giving it up?
He does if you follow her route. In Jess's ending he offers to make that the last wish he ever performs but Jess turns him down on that offer.
Regardless of the fact that Vayne can potentially end up with anyone in the True Companions, members of said group seem to have a fondness of citing his interests towards another character (Jess, in her second-to-last and final Character Quests, for example). Or... lack thereof, in Pamela's case. "This is Vayne we're talking about; that's impossible!~"
Like You Would Really Do It: Like anyone would die. Really. Really, there's no sarcasm in this statement. The bad ending doesn't count.
"A Quiet Giddiness", the final school theme that plays during the later, Mood Whiplash chapters of the game. A technically excellent song, but the sheer trepidation of it and the fact that it's played everywhere you go in school from then on, in contrast to the first, almost absurdly upbeat school theme, makes it quite hard to bear during those moments when everything's falling apart.
Vayne's special attacks all involve shadows, lots and lots of sharp blades, creepy red eyes, and surprisingly violent battle quotes. So it makes sense that the final boss is a horrible mass of red eyes that cry black gunk. Oh, and his true power is pretty scary too.
When Isolde kills one of your friends to force Vayne's powers to surface, you have to think: what if Vayne wasn't able to bring him/her back, and Isolde took the leap from slightly unbalanced teacher to murderer? Even worse than that, she didn't even flinch when she killed them. If Vayne couldn't wish him/her back to life, what was to stop Isolde from murdering all of them right then and there to keep said murder a secret?
Player Punch: Before the second boss battle with her, Isolde crosses the Moral Event Horizon and kills one of your party members to force Vayne to use his powers to revive them, proving he's a Mana. Which party member gets killed depends on which one's character quests you did, which probably means that you have an attachment to that character. Of course, since Vayne's the Mana of Wishes, they get resurrected quickly, which can lend itself to Narm, but damn if that didn't piss the party off. And the player too, maybe.
They Changed It, Now It Sucks: A fairly-often heard call from some parts of the fandom concerning changes to some names in the English version, specifically Philomel Hartung to Jessica Philomel, and Gunnar Damm to Flay Gunnar. Others argue that these are Woolseyisms, of course, as the reasons for the changes are obvious; "Philomel"'s name was shortened to "Philo" (or "Phil", if you like) in the original version which leads to rather obvious problems, and NIS America probably didn't want a character to sound like he had a curseword for a last name. Some fans just can't be satisfied with any change, however.
It has to be granted that this is exacerbated a little if you play with the Japanese audio on; since NIS America didn't have the time, money or manpower to re-record any Japanese dialogue, the unedited names still show up, leading to a little bit of annoying dissonance between the text and the speech. This can simply be solved by not using Japanese audio or turning the event audio off completely, though.
The above two are the most often-cited examples, but other characters went through technical changes compared to the initial published English names Gust gave the characters - but these are even less complained about because the Woolseyizing is even more obvious. Anna's last name was "changed" to Lemouri to match the katakana of her name (レムリ); the given spelling in Japanese materials is "Laemmle", but that doesn't even match the katakana (it'd be pronounced similarly to "ray-me" with that spelling). Nikki was originally "Titil Mimi Nike Mele", but she was always called ニケ; this is very close in pronunciation to "Nikki" so any change to her full name is essentially semantic. Most other changes are in line with this - not the exact spelling that Gust initially printed, but often so close yet subtly cleaned up for an English reader that any argument really becomes semantic.
Some aspects of the localization are just plain bad, though. Skills are mistranslated and/or translated inconsistently. (Why does Shade Shift become Jade Shift in battle?) Some liberties were taken with the dialog in places, occasionally leading to awkward or out of character phrasing. ("Your blind allegiance will be your undoing?" That sounds like something Flay might say, not Vayne. The original line was just "Why are you doing this?") Grammatical errors abound. And so on.
That One Boss: The second round against the blue-haired teacher. She basically spam activates a thunder attack that puts alot of cards on the battle sequence, clogging up your moves, and does a two round mass-kill attack, unless you can block it, or use defensive supports. You need a ton of mass revive items, and even then, you'd probably still die.
Goddamned Boss: ZweisMunde (literally "two worlds") is actually a fun boss, but really loves to use Interface Screw attacks. One of them turns all your healing echo (and other multi-card techs) into its own multi-card attacks. Another one swaps out your entire team.
The Scrappy: Tony. The guy is your typical stuck up asshole who has a grudge against the protagonists. His only redeeming quality is that he's so pathetic it's funny and that he's a threat in boss fights.