In this series, Fate comes off as an unstable Yandere, who uses threats of the TSAB ON EARTH SOIL - forgetting that Earth is not under it's 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 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. Word of God has clarified, however, 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.
However, most people in return point out that the writer did a horrible job of showing this, and the chapter itself (unrelated to the rest of the story) felt like it was created just to shit on the Sailor Moon side some more.
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.
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. 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.