If you are seeing an underpayment penalty included as part of your tax return, it simply means that you did not have enough Federal taxes withheld from your W-2 income to pay your taxes.
The Federal income tax system is a 'pay as you go' system, you cannot simply settle up when you file your return without including a penalty if you did not withhold enough.
To read more, see: Why am I getting an underpayment penalty?
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