The tax that was withheld was only an estimated amount of tax. If you were younger than 59 1/2 you also have a 10% early withdrawal penalty. Just like when you have tax withheld from your paychecks and tax is withheld, you enter all of the information including the amount of income and amount of tax withheld...The software calculates whether you had too much withheld and you get a refund, or if you had too little tax withheld, you could still owe.
The tax withheld on your retirement distribution is an estimate of taxes due on the distribution amount.
In general, 20% is withheld for Federal Taxes on a distribution from a retirement account, unless you selected a higher amount.
If you are in a different tax bracket and depending on your other tax return items (deductions and credits), the 20% withholding may not have been enough.
If it was not enough, TurboTax will take that into account, along with all of your other tax details and determine if you have a tax amount due to be paid,or a refund due to you.
Rest assured, if you input your Form 1099-R correctly (doublecheck your entries and make sure you entered your Federal Withholding amount correctly), the program will properly calculate your amount due.