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.
I want to be clear.
I don't think you are having more taxes taken out of (withheld) from your retirement distributions. You would have to notify your broker in writing for them to do that.
It sounds like you owe taxes, even though you had taxes withheld from your retirement distributing.
You can check some things on your tax return.
Your retirement income is listed in boxes 4a, 5a and 6a
Taxable income is retirement income is listed is in 4b, 5b and 6b
These are the most common causes of additional taxes on retirement, there may be others.
Please contact us again with any additional questions.