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When you enter your form 1099-Q and enter no education expenses to justify the distribution, TurboTax will populate form 5329 and automatically calculate the tax and the penalty, which will be added to your tax liability.
You say you "paid the penalty". How did you do that and did you get a form for it. You don't usually pay the penalty (and tax) until you actually file your tax return. You want to be sure to get credit for any withholding you had done. Withholding on a 529 distribution is unusual (there is no place on form 1099-Q for tax/penalty withholding).
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