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.
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.
Critical Research Failure: In the final chapter, one of the youma, who happens to be capable of Voluntary Shapeshifting, uses Reinforce's form to get close to Hayate and Signum. Unfortunately for her, she exposes herself by addressing them as "you two" while Signum was in a unison with Rein Zwei. Rein Zwei called her out on it, and Signum took her out.
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.