If you are referring to a rental situation, you should not enter any of the mortgage interest amount on your Schedule A. You should ONLY enter the Form 1098 mortgage interest amount under the Rental. The program will then allocate and pro-rate the mortgage interest between rental and personal based on the information of percentage of usage you provided. The amounts should be allocated correctly on your tax returns. ( Schedule E for rental and schedule A for personal)
I will suggest you to take out the mortgage interest amount on Schedule A, revisit the rental expense including mortgage interest portion. The program should update and do the math correctly.
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