Did you run all the steps of the interview or did you exit early? When entering a 1099-R from a Roth withdrawal, you must keep hitting continue to run all the steps of the interview. You will eventually be asked for the total of prior year contributions and conversions, and prior year withdrawals. (Any current year contributions are entered in the Roth IRA section on the deductions page.) If your withdrawal is less than your current balance of contributions (contributions minus previous withdrawals) it won't be taxable, but Turbotax doesn't know this unless you give it the details.
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