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.