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Use the TurboTax Audit Support Center and speak with an agent to get assistance with the IRS notice you received - https://support.turbotax.intuit.com/irs-notice/audit-support/
You would have a hard time providing it was a program error since that has apparently not been widely experienced.
One thing I've seen happen is if you imported any info from your bank it also imported the 1098 and Mortgage interest. Then you also manually entered it.
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