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The IRS should catch that and send it back to you. Do you have proof the auto deduction came out of your bank account in addition to the check? Double check your bank statement. It might have just been the Turbo Tax fees.
Check to make sure the amount that was deducted "with auto deduction on turbo tax" was not just your TurboTax fees instead of the tax due to the IRS.
How can I see my TurboTax fees?
https://ttlc.intuit.com/questions/2565973-how-do-i-review-my-fees-in-turbotax-online
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