@kaminomikan
That comes down to Spica not understanding the issue and did not report the heroes gender, and only the conclusion she came too about the hero´s relationship with the girls.
Spica knows that the hero is a girl, and she assumed she misunderstood the problem the hero liked other girls ( being a playboy, instead of being a lesbian )
Takeing a child directly from an orphanage and expecting them to be flawless spies is a recipe for disaster.
Also, I could be remembering wrong, it was a while since I read the novel but I think the hero was referred to as "they/them" or "the hero" and not he/she when others talk about them.
IIRC It was actually a pretty big plot twist for her to be revealed as a girl.
@Knighto
True, but you have to remember that Spica´s reports always goes through a middleman before it reaches the MC and that she is a little girl who is prone to mistakes like everyone else.
It's possible that she did say "she" instead of "he" when making the report but that it got lost in translation.
Not to mention we were not shown the heroes explanation at all and just the outcome of it.
(it's possible that it was explained properly and they just did not show it to save space, I would have to go and re-read the novel to make sure though... )
IMO that doesn't make it bad writing anyway, but at the end of the day "bad writing" is about a person's feelings and expectations about a story and comes down to a case by case basis.
So it could just be that we have different standards when reading.