Please see this answer from AndreaG:
I went through this process in Turbo Tax, the online self employed version; I am not sure which version you are using. There are multiple ways to enter the real estate taxes in to the business use of home section. I entered in my square footage and entered in the entire expense. I also went to the deductions and credits section for itemized deductions and entered in the entire expense under the real estate tax category.
When I looked at the Form 1040, it calculated the Schedule A deduction correctly and there wasnt any doubling up. You might want to retrace your steps in the business use of home section as well as the deductions and credits section to see if you can determine what happened.
