I don't really see the problem in a fictional character's attitude on another fictional character being a big deal, I think the human race is becoming a little TOO sensitive these days.
The main issue that I've seen is that using "it" to refer to a person is going to upset non-binary or otherwise trans individuals for understandable reasons, given that referring to them by "it" is a way to bully and dehumanize them. Some non-binary individuals are okay with being referred to by "it," as they feel nothing else fits. But for the most part, as far as I am aware, using that without being told they're fine with it is usually a jerk thing to do.
The thing is that these stories do not exist in a vacuum. I can look at the story all by itself, sure, I can look at the characters and see how they react to things because of the world they live in, okay. But this world and these characters were still constructed by someone in reality. Someone who is going to have various biases whether they're conscious of them or not and the people those biases are most pertinent to are going to see that in their writing.
So, I can definitely see why some are angry regards Sera saying "it."
Hopefully some manner of clarification + positive development will occur when the game is out and we can see for ourselves.