Deposited money into traditional IRA to repay 1/3 of my covid-19 distribution and TT is saying I owe a penalty for excess contributions.

Repaid 1/3 of my covid-19 distribution after Jan. 2023. When I put this under traditional IRA contribution and mark that it is a repayment, it is still saying I owe a penalty for excess contribution. I did mark the box that it is a repayment. Why is it saying this?