To make sure I understand your question, you said you filed your original return and were expecting a refund; however, you received a letter from the IRS advising you owe money? In order to answer this question we would need additional information. What type of notice or letter did you receive?
Here are some links to review to assist you when you receive an IRS notice or letter:
I got a letter or notice from the IRS
What to Do if You Get an IRS Notice
Understanding Your IRS Notice or Letter
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