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Since your income is exempt from tax under IRC 131, you should be able to claim that the withholding is refundable as overpayment.
Form 1040, line 73, is the line on the form for overpayment withholdings such as these. You can claim the withholdings as additional taxes withheld, and request a refund when your return is processed.
i would attach an explanation, along with a cite to the Notice and proof that your payment indeed qualifies for the treatment. IRS should process the overpayment and refund in the normal course of business.
From the 1040 instructions for line 73:
"If you made a tax payment thatdoesn't belong on any other line, includethe payment on line 73. Check box dand enter “Tax” in the space next to thatbox."
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