You will not be paying taxes on the income twice. You report on your tax return all income including the 1099-R you should have received for the retirement income. On that 1099-R you will see and subsequently enter in TurboTax, any taxes that were withheld so that you get credit for those payments. At the end, if you have paid more than your tax liability, you will get a refund. If you have not paid in enough you will owe a tax payment by 15 Apr 2020.
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