Your best bet is to contact the IRS and see if they can re-apply the payment, as it appears you accidentally misapplied the payment. When you call, be sure you have the information of the payment in question in hand so that they can find the payment and assist you in re-applying it.
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To call the IRS:IRS: 800-829-1040 hours 7 AM - 7 PM local time Mon-Fri
Listen to each menu before making the selection.
First choose your language. Press 1 for English.
Then do NOT choose the first choice re: "Refund", or it will send you to an automated phone line.
Instead, press 2 for "personal income tax".
Then press 1 for "form, tax history, or payment".
Then press 3 "for all other questions."
Then press 2 "for all other questions." It should then transfer you to an agent.