There have been a lot of queries regarding the fact Mew is referred to by both 'he' and 'she' in chapter 61 - most of them noticing one instance and assuming it's some kind of a typo.
It is not a typo: Mewtwo consistently uses 'she', while Chaletwo and Mark's narration consistently use 'he'. (And May, you may also notice, uses 'it' - which means in this chapter the same character is referred to by all three standard English third-person singular personal pronouns, something I quite enjoy.) This is because in the world of this fic, all legendaries who are genderless in the games are biologically sexless single-individual species that don't have a gender as we know it. Some of them - like Chaletwo - prefer to be referred to by one particular pronoun anyway; others don't, and much like with Pokémon nicknames, the pronoun used in any given instance is up to the speaker. Mew is one such legendary.
This is not a new thing; I've been consciously writing it that way since at least the beginning of the HMMRCIG if not longer, and outside the fic I've been explaining this to readers for about that amount of time. The first time I found occasion to actually bring it up in-story, however, was the first time the opposite of the usual pronoun was actually used for a legendary: chapter 51, where Entei used 'she' for Mew. I threw in a paragraph of Mark remembering that Mew has no grammatical gender preference - kind of out of nowhere, but it was at least intended to introduce the concept to readers so they wouldn't be confused. And it seemed to work: I can't recall anyone expressing confusion over it then, so I actually was kind of surprised by how many people were completely puzzled when the same thing happened in chapter 61.
Now, I said I'd been consciously writing it this way since at least the beginning of the HMMRCIG. If this were a newer concept, it would probably be a bit more refined and informed by modern ideas about gender - but the fact it is old means that pronoun use has been an active part of the characterization for ages. So now that I've found an excuse to ramble about that, I will! :D
If you were to reread chapters nine and ten or Mew's random appearance in chapter 13 (but please don't), for instance, you'd notice Mark's narration awkwardly avoids using any pronouns for Mew as far as possible but goes with "it" where a pronoun is absolutely necessary. However, Chaletwo has always referred to Mew as 'him' - in fact, Chaletwo uses 'he' for every legendary that doesn't expressly prefer the feminine. It just seemed like what he'd do: he wants things to be simple and easy and doesn't like to think about them too much, so he made a rule - using the same pronoun he prefers for himself - and just sticks with that. And Mark, since chapter 25, has simply gone along with Chaletwo's pronouns for everyone, including Mew. (When he started not going along with everything Chaletwo said and did, it didn't occur to him to change his pronoun use in protest, but on reflection that would have been rather amusing.)
May, meanwhile, uses 'it' for all such legendaries, because as far as she's concerned that's just the correct pronoun for something genderless. Its potentially 'dehumanizing' properties don't bother her because she's not the most tone-sensitive person in the world. (Who would've thought?) I don't think anybody has ever commented on May's use of 'it' for legendaries Mark and Chaletwo are calling 'him', which just goes to show that people are perfectly capable of seeing the same character referred to by two different pronouns as long as they don't happen to be 'he' and 'she'.
Entei was an interesting case - it felt like he would refer to Mew as 'her', but as I wrote him I started to realize that as part of his general condescension he has shades of a kind of pseudo-sexism - he uses 'she' for smaller, less imposing legendaries. Although Suicune for instance also has no preference, my mental simulation of Entei found it
absurd to call
him 'her', because Suicune is his
equal. He goes through all the motions of respecting Mew, but doesn't think anything of just going and making a plan to stop the thing that Mew doesn't want to be stopped - where Chaletwo keeps justifying his decision to disobey Mew with the greater good and Mew just being tired and not wanting to live anymore, Entei has no real impulse to care about Mew's opinion in the first place. In some way, calling Mew 'her' is because he doesn't think much of her and uses it as a kind of way to designate her as a different class from himself that he can be elitist towards.
Mewtwo, on the other hand, began to use 'she' for Mew to differentiate himself from her as part of his journey towards realizing that he was his own person with a right to exist independently of Mew. (Side note: I really liked writing Mewtwo and how he's dealt with his issues in the twenty-seven years since he was created.)
I've also written some backstory material from Mew's point of view that alternates between using 'he' and 'she' in the narration between scenes. If you found it confusing in chapter 61, just wait until you read
that.