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Hi from Just Answer. There are a couple of things you can do to fix this.
One is wait for IRS to identify the overpayment and refund the excess. Not my favorite solution.
The second is an amended return to report the overpayment. You have to file it on paper, but the amendment will allow you to report the overpayment and request a refund.
I like to provide copies of the payment receipts to prove IRS got paid twice. They will process the amendment and refund your overpayment in a few weeks.
Thanks for asking at Just Answer. Positive feedback is appreciated. I'm PDtax.