When I enter mortgage interest for my home office, it looks like it is taking the mortgage interest deduction twice

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When you enter your mortgage interest for your home office deduction, you do not also need to enter it as a deduction for your home. Turbo Tax will calculate the "business" percentage to be reported of your home office expense and will carry the balance of your Mortgage Interest to your Schedule A.

So, just go to your home information and delete the mortgage interest you entered there. That will do away with the duplication.