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Withholding on a 1099-R works in the same way it does on your W-2. It is taken out to pay the tax as it accrues. At the end of the year, there is a reconciliation. If you paid in too much, you get a refund. If too little was withheld, you pay.
If you had and early distribution from a 401k, there is a 10% penalty for taking it. This is in addition to any tax that you have to pay on the income. The income is added to the rest of your income and taxed at the Federal rate. If they only withheld 10%, then that covers the penalty only. TurboTax is just letting you know that there is a penalty.
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