The word is “die Magd” and it means “maid”. The -chen makes in diminutive, so the original meaning was “little maid”. But today it means just “girl”. But beause all -chen diminutives are neuter, Mädchen is neuter too, even though the original word (Magd) was appropriately feminine.
Personal pronouns such as er, sie, es refer back to something earlier in the conversation.
In this case, sie might refer to (say) "Julia", who is female and is thus referred to by the feminine pronoun sie. Now you are saying something about her, and the thing you are saying it: she is a girl.
The fact that the new information involves a neuter word is not related to the fact that the older information involves someone female.
The sie at the beginning refers not forwards to ein Mädchen, but backwards to somebody who had been mentioned before -- perhaps Julia.
So the natural gender is used, feminine sie.
If the previous sentence had used a neuter noun such as ein Kind or ein Mädchen, then es would have been appropriate to refer back to it.
Firstly, the word Mädchen is neuter, not masculine, so even if it was in accusative, it would be ein and not einen. Secondly, the verb sein (ist, to be) is not transitive: It is a special verb (you can understand it for example as a connection of two subjects) which takes both nouns in nominative.
Because the words Frau, Mann, Mädchen belong to different grammatical genders (categories).
Frau "woman" is a feminine word and takes eine
Mann "man" is a masculine word and takes ein
Mädchen "girl" is a neuter word and takes ein as well. (Note that the grammatical gender is not related to the real-life gender here.)
ein is used before nouns that are grammatically masculine and before nouns that are grammatically feminine.
eine is used before nouns that are grammatically feminine.
The noun Mädchen is grammatically neuter -- as you can see, its grammatical gender has nothing to do with the natural gender of girls.
Much as a spoon -- der Löffel -- is grammatically masculine even though spoons are not male or masculine.
Grammatical gender is mostly arbitrary: just something to memorise.
"I just met someone called Kim". "Oh, boy or girl?" "She's a girl."
Also, it's worth pointing out that English can use "It is" in some situations.
Hospital nurse: "It's a girl!"
"Dad, there is someone at the door" Child opens door. Dad: "Who is it?" Child: "Oh, it's just a bunch of politicians canvassing for your vote." Dad: Slam!
Earlier in the lesson Sie ein Mädchen was translated to you are a girl.
Sie ein Mädchen is not a correct sentence -- there is no verb.
"You are a girl" could be Sie sind ein Mädchen (if you are addressing the girl formally -- perhaps she is 17 and nearly an adult, for example).
But sie ist can never mean "you are".