It's unusual for a school to include books and supplies in Box 1 of the 1098-T, but not unheard of.
Q. Do I need to deduct the actual amount I spent on books and supplies from my total payment in Box 1 and enter that amount separately?
A. No. It's actually easier if they are included. TurboTax is telling you that there were no net qualified education expenses is unrelated to that issue. The usual reason is that the box 5 amount is more than box 1.