You only need to enter your mortgage interest in the 1098 section. TurboTax will automatically bring the mortgage interest from the 1098 section into the home office section and allocate the amount that should be used for the home office to your schedule C and leave the rest on your schedule A.
Did you enter it in both locations or do you just see it in both locations? If you are NOT itemizing then this will not affect anything. If you are itemizing, entering it twice could cause a duplicate mortgage interest deduction. If you are itemizing your return, then you will need to go back through the Home Office section to delete your mortgage interest entries so it is not duplicated.
If you just see it in both locations and only entered it in the home office area, then you are just seeing it on the summary screen and it will not affect your return.
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