If you are under 59 1/2 year old you are getting the income tax added plus a 10% early withdrawal penalty. Also state taxes if you are in a taxed state.
Depending on your tax rate, you may have not had enough taxes withheld. For example someone in the 25% Federal Tax bracket would need to have 35% Federal Taxes withheld to break-even.
Check your withholding to see what percentage it is of the total in Box 1 of the 1099R's.