IRS missing my 1099R withholding from a Financial Institution-TY 2024

The IRS sent you a letter questioning the taxes withheld on your Form 1099-R?  If so, look at the Form 1099-R you received.  Is there an amount in box 4 for federal taxes withheld?  If so, did you enter that amount on your federal tax return when entering your Form 1099-R?

If you did it would show up on your federal tax return, Form 1040 on Line 25b.

You may mean that you reported the tax withheld but the IRS is saying they have no record of it. If so, you can send them a copy of the 1099-R form. It is possible the company that prepared it didn't submit the copy to the IRS.