Do you show federal tax withheld on your 1099-R?
When you take a withdrawal from a retirement plan, you generally have money withheld, but you don't know if it was enough until you file your taxes. Your tax bracket is calculated on your total income, and depending on the amount of the withdrawal, it may move you into a higher tax bracket.
Additionally, there is a 10% penalty for taking the money out prior to age 59 1/2, as you said.
If you had other income, the federal due could be due to insufficient withholdings from that income. You have to look at the whole picture to determine why you have additional federal tax due