There hasn't been any official confirmation on if Chrona is a boy or girl. In the manga, Chrona uses 'boku' and the other MALE ways to address her/himself. And the manga's websites lists Chrona's gender as 'unknown.' And none of the characters have come out and said which gender Chrona is... scanlators have just gone with it and guessed that Chrona is a girl (though in early chapters they went that she was a boy)
So, officially, dunno. People use the excuse that Chrona said he/she wasn't good with talking with girls early on, to argue she must be a boy. But he/she doesn't really seem good with talking with anyone or either gender.
I don't remember if or when Medusa said daughter or not-- but in the original Japanese she could have easily just said 'child' and the scanlators went with the daughter translation...
So, scanlators translations & fansubbers = not the best to figure out Chrona's gender