1) Panic, because the book was supposed to be YA.
3) Ask for a bunch of volunteers to read the book for you. Look for volunteers who read MG and YA regularly, who can spot the difference between the two.
4) Convince yourself in the meantime that everyone’s feedback will come back agreeing with your original intentions and all will be well.
5) Receive feedback that unanimously agrees you’ve written an MG a book, not a YA one.
7) Realise that editing the book to fit MG conventions will take a LOT less work than editing it to fit YA conventions, and stop crying.
8) Plan your attack on the manuscript.
…But in all seriousness, it’s really important to listen to your readers in matters of genre. As the writer, you always see what you meant to write, and that can really cloud your perception of genre. “I set out to write an urban fantasy that defies conventions and does X, Y and Z instead of A, B and C.” Well, cool, but the result probably won’t be urban fantasy, because the entire point of genre conventions is that the stories in that genre conform to them for the most part. So listen to your readers. (I’ve actually seen several cases of authors who didn’t, and it never works out well sales-wise.) Even if you thought you were conforming entirely to a genre’s conventions, if readers tell you you haven’t, it doesn’t matter what you intended.
Listen to your beta readers, take a deep breath, and dive back into those edits.