Nanoha sees the incident in Episode 3 of the original Magical Girl Lyrical Nanoha, in which her failing to act on a possible sighting of a Jewel Seed, resulting in damage to Uminari City, as a failure that motivates herself to push herself as much as she can, resulting in her being a Workaholic averse to rest.
In this series, Fate comes off as an unstable Yandere, who uses threats of TSAB interference ON EARTH SOIL - forgetting that Earth is not under its jurisdiction, all just because she's jealous of a relationship that a man had with Nanoha in a past life. The author treats this as if she's in the right.
Was Nanoha justified in harshly calling the Queen out on how she raised Serenity? Additionally, was this in character for Nanoha, who is admittedly more responsible than Usagi or Serenity, or was this contrary to someone who would "befriend" her enemies? Or was Nanoha pushed too far with memories of her past life returning and called her out due to a Despair Event Horizon?
Vivio defeating Chibi-Usa and causing her and her alternate timeline to disappear was also a controversial action, especially since it was essentially killing her. Furthermore, the chapter itself is unrelated to the rest of the story and felt like it was created just to shit on the Sailor Moon side some more. Word of God has clarified that Picoha was the aggressor, attacking without stating her intent, and Vivio tried to defeat her non-lethally, without knowing what would happen to her.
Moral Event Horizon: Precia crosses this in even Fate's eyes when she attacks Alicia for refusing to stand aside and let her continue to torture Fate.
Plot-Induced Stupidity: A lot of the early plot revolves around Fate and the Sailor Moon cast coming to the worst conclusions possible and being utterly unwilling to talk to each other clearly.
Strawman Has a Point: At one point, Luna is stated to be far more sympathetic to Serenity committing suicide at the end of the Moon Kingdom, which rendered the sacrifices of Kamen and Mina pointless. While this is meant to show that Luna is out of touch with reality (and for the most part she is), the point she raises is perfectly correct: Nanoha had been a member of the TSAB and was trained to not sacrifice herself pointlessly, had known years of battles against the forces of evil, and held herself to such high standards that she literally worked herself into the hospital, and is judging a girl raised in a completely different environment with a completely different set of priorities up until that point by said standards, which aren't exactly fair to Serenity, a girl with no experience of how evil and cruel the world could be who just watched everything she had ever known and loved get murdered violently by eldritch abominations.
Seeing as Chibi-Usa is Usagi's daughter, having her enter the picture would have made for some excellent plot points, not the least of which making Nanoha and Fate (who would undoubtedly be unwilling to make an innocent child die) have second thoughts about getting together. But the author not only says that she will NOT be appearing in the story, but she gets unceremoniously killed off in an omake that honestly makes it seem like, to the author, Chibi-Usa is The Scrappy.
Word of God had it that while Nanoha feels an initial attraction to Mamoru due to their romance in the past, she isn't guaranteed to love him in the present. The idea of Nanoha and Mamoru having to reconcile their lingering past life feelings while Nanoha realizes her current love for Fate could have been very interesting to see, but it's reduced to Nanoha largely ignoring Mamoru after one poor date and Mamoru being left on his own to come to terms with the woman he loved not returning his feelings.
A lot of good story potential the inclusion of Mistress 9 and the Death Busters might have provided (especially considering they'd be competing with Beryl for dominion over Earth) was squandered when they were abruptly introduced in one chapter and all killed off before they even really had a chance to launch their evil schemes. Mistress 9 in particular was hinted for quite a few chapters, with Hotaru suffering the effects of her possession, but is pretty quickly disposed of by Mars and Shamal.
The entire premise of the senshi having to work as a team under a different leader than Usagi and learn to get along with the TSAB is a fascinating one, but most of the TSAB ignore the senshi besides mentions of bringing them into battle, the senshi largely ignore one another, and Nanoha doesn't interact with them very much outside of training sessions.
Nanoha brutally reams Princess Serenity for rendering the sacrifices of her bodyguards pointless by committing suicide... forgetting that she was an ordinary untrained 14-year old who had already been cornered by enemies powerful enough to kill the four most elite warriors in the entire kingdom and wipe out the rest of it to the last man.
Mamoru is written as someone so hung up on loving a version of Nanoha he imagined from memories of their pasts that he can't see her for who she is in her present life. While that's insensitive of him, it's also mentioned that to him, the memories of his past are pretty much all he's had to go on — presumably as in canon, Mamoru lost his entire family in a car accident, which also gave him amnesia. That means he spent most of his life not only without a family or memories of his childhood in this life, but the circumstances of this AU mean he doesn't have the friendship with the senshi he had in the series. His clinging to memories of who Nanoha once was come across not so much as him being unwilling to acknowledge that Serenity is now someone entirely different as him clinging to vivid memories of a time when he had love and was happy. While he does get Pair the Spares at the end with Rei, his overall treatment in the story comes across as a bit callous, especially since there were two omakes dedicated to him being passed off to other female admirers (one of whom was Beryl) without his consent and it was entirely Played for Laughs.
While Luna is legitimately backwards in her views about the Moon Kingdom existing, she still genuinely wants to help the senshi and protect the planet. Everyone's exasperation and constant belittling of her may be a bit easier to take if (A) there was any indication that someone at least tried to explain to her that she was operating under misconceptions about the relevancy of the Moon Kingdom and (B) if the characters were willing to admit that not everything she did was 100% her fault (the initial conflict between the senshi and Fate is treated as being completely Luna's fault, despite it being Fate who initially acted aggressively and didn't think to simply explain "Nanoha is injured and needs rest, but I can put you in contact with some people who can help, in the meantime").
Nanoha is treated as rather put-upon for having to deal with the senshi, Luna, and Mamoru treating her as if she were still Serenity. She never actually addresses this with them though, until she loses her temper with Mamoru on the moon, at a time when all of them are in very tense places. Despite being talked up as an excellent trainer, she also opts to put the senshi through the very Training from Hell she canonically realized was ineffective and hardly interacts with the senshi beyond that, much less makes any effort to work with them as a team outside of combat. That it's openly admitted that she has no hobbies or interests outside of her work also makes her come across as a Flat Character.
A lot of Fate's actions early on in the story are meant to be seen as her protecting Nanoha from needless stress, they come across as borderline yandere at times (her fending off Mamoru and Luna attacking her is understandable. Her contemplating having them kidnapped off of Earth and taken to a planet where the TSAB has jurisdiction is... less so). It doesn't help that her incredibly vague explanation to Luna why Nanoha couldn't help fight Beryl (Luna made it clear the fate of the planet was in jeopardy, Fate doesn't say that Nanoha's out of commission or that the people she can pass Luna's message to are fully-trained, very powerful magical girls) caused the initial conflict between herself and the senshi. When Luna makes it clear she's not happy with what she's told, Fate promptly jumps to threatening Luna, which is part of the reason why Luna was convinced Fate was a "dark senshi". It doesn't help that nobody, not even Fate herself, acknowledges her part in the subsequent misunderstanding.
Writer on Board: Bissek goes out of his way to give the Senshi the short end of the stick, using an altered canon that incorporates elements cherry-picked from both manga and anime canon with the goal of making the Senshi look as weak, useless, and morally bankrupt as possible. note This diminishes after the first arc but is nonetheless present. The whole issue with Serenity killing herself, for instance, is taken from the manga, while the Senshi themselves display abilities only on par with their heavily-nerfed anime counterparts. The villains that the Senshi struggled with for over a year are also trivially dispatched within weeks of the TSAB showing up (granted, the Senshi took out the same number of Dark Generals as the TSAB, and Nephrite only lost to Vita via a Groin Attack he didn't expect). And let's not even get started on the Picoha omake.