When you took the distribution, you had tax withheld, just like your employer always withheld tax from your paychecks. But that was an estimate of the tax you would owe for that money. The software calculates the final amount you still owe or the amount you get as a refund after all of your income is entered into the tax software. You may be combining that retirement income with other income such as income from working, Social Security, investment income, etc. etc.
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