When I enter the correct amount of mortgage interest from form 1098, it results in an incorrect mortgage deduction because it's adding it to the rental mortgage interest

If you are renting out part of your house, then part of your interest is on Sch E and the remainder goes on Sch A. When you have the program do the math for you, it automatically enters the correct portion on each form so you do not enter your personal portion again.

I am going to assume you rent part of your home out. Return to the rental section and check if you chose to do the math or let the program. If you enter the pro-rated rental expenses, you will need to enter your personal interest in sch A. Otherwise, don't. My guess is that you let the program do the math and entered mortgage interest for sch A. You can't do both.