"Deeper issues" refers to problems or concerns that go beyond surface-level or immediate issues. It suggests that there are underlying, more significant problems that need to be addressed or understood. Full definition
It will help you understand that adrenal fatigue arises from deeper issues of how we approach other people, our attitude about life in general, and our views of self. (adrenalfatiguesyndrome.com)
He specializes also in working with deeper issues from childhood. (psychologytoday.com)
There are some very deep issues in this novel, much deeper than they may appear on the surface. (splashdownbooks.com)