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.
