Most likely it is because the estimated tax payments you made were insufficient to cover this year's tax liability.
The IRS generally assesses a penalty if more than $1000 is owed after prepayments and withholding are applied to the current year's tax bill. In other words - if you owe more than $1000 this year, the underpayment penalty was assessed because the estimated payments were not enough to cover your tax liability for this year.
