Having a balance due from an amended return does not mean that there is a problem with your amended return.
Without knowing the details of your return, there is no way for me to know why
you owe part of your refund back to the IRS (if you received a refund on your original return).
However, a common issue would be that if you added another W-2, then the increase in income may have decreased a credit you received or the W-2 did not have enough taxes withheld to cover the increase in income tax when you added the additional income.
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