I payed my taxes but IRS sent me a letter asking for amount I payed

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If you have proof of payment, such as a canceled check, bank or credit card statement showing the payment to the IRS, or a confirmation number when you paid the amount owed on the IRS Payment website, then contact the IRS using the information in the IRS letter you received to resolve this issue.

How did you pay it? Did you mail a check? It might have crossed in the mail. Or you might have sent the check in with the wrong voucher slip. It should be a single 1040V voucher. If you send in a 1040ES slip that is for an Estimated Payment for NEXT year and didn't get applied to 2021 balance due. Check your IRS account to see if they got it. You need to send a copy of the check or bank statement showing the payment was paid.
https://www.irs.gov/payments/your-online-account