What did you actually do?
1. You contributed money to the HSA in 2019, right?
2. Then in 2020, you contributed more money to the HSA for year 2019, which out your over the 2019 limit - is that right?
3. If so, this should have appeared on your 2019 return - did it not? Did you not enter this 2020 contribution for 2019 onto your 2019 return?
4. Since you apparently withdrew the excess contribution for 2019 before the due date in 2020, then in the 2020 HSA interview, when you are asked "Did you overfund your HSA in 2019?", you would answer "NO", because the question really wants to know if you carried over your excess contributions from 2019 to 2020 which you did not.
Do I understand your situation correctly? If not, come back and tell me what really happened...