This is actually fairly common. There are usually two reasons for this happening:
You accidently paid the wrong people. Meaning you owed the IRS but made a payment to the State (FTB) or vice versa. Check your payment receipts.
or
You filed a joint return but when it came time to make the payment you listed the spouse’s name (second name on the return) as the person making the payment. When this happens the IRS/State does not post the payment to the correct account. You will need to call the number on the letter and have your payment receipt handy. It is an easy fix but does require a phone call.