I know this thread is old but I am in the same situation and struggling to fix it.
In 2019 i made an overcontribution and excess was returned. Because they payment was made to me in 2020, i had no 1099R in 2019 to prove my reported numbers. Due to this the government accepted my penalty and income tax payment but rejected my withholding claim causing me to pay it after filing.
Since the payment was made to me in 2020, i received my 1099R with the year 2020 on it and code PJ in box 7. I tried submitting a 2019 amended including this proof of 1099R but it was rejected. So it sounds like i need to file a 2020 amended to report my excess withholding and trigger my refund?
