If there is one thing I have learned in the revision process it’s that you can’t hide your “problem areas”. If you (meaning me) think there is a major issue or problem in your novel, there probably is. I ignored two major issues in order to just finish writing a first draft of my YA novel and lo and behold at the end of the first draft there they still were.
Sometimes it is good to ignore problems in order to churn out that first rough draft, but you can’t ignore them forever. Other people, in this case my very savy agent, will see them too. On a positive note, these problems are good because they represent an opening, an opportunity to vastly improve your book, and the good news is, you already know what they are.
Ideas In Things 
“I ignored two major issues in order to just finish writing a first draft of my YA novel…”
Key word: Finish.
It pleases me so much to see that you put those errors aside and continued on in order to complete that rough draft. There are far too many writers out there who fail to finish anything at all because they can’t ignore a mistake. You did a great job by ignoring it, and now you can go back and fix it knowing you’ve got something solid to work with.
My noveling blog, Uninvoked, was my first novel ever when I first started writing it. Before then I did what every other beginner writer does. I’d get a few thousand words in, realize I made a mistake, and self-edit until I forgot what I’d intended to do. Uninvoked is my first complete novel, and I hope to gain some readership through my blog.
I hope you continue to fight off the internal editor when you write that first draft, and that you remember to turn it on before sending it to your agent. 😉
Best of luck to you.