How did you pay in April? Was it a payment with an extension that is on 1040 schedule 3 line 10 and goes to 1040 line 31? Or where did it show up on your return?
Did you send it with a 1040ES slip? That would be for a quarterly estimated payment for NEXT year 2025. It may be applied to the wrong year. You probably should look up your IRS account to see if they got it and where they applied it.
Is the letter for the same amount you already paid? Or they could have changed your return so you owe more.