Which brokerage firm you have? In my case, I did inform Fidelity in last August that I have over contribution situation but they told me I can't file return of excess until I get both companies W2 (which I had to wait till Jan 20222).
Anyways, good that you got 1099-R, I think as per MinhT1, TT will flag it as warning (about 401k over contribution) but we should ignore it, as long as you enter 1099-R showing your income as taxable. I would try to get corrected 1099-R if possible, $1 extra shouldn't have any negative impact though. This is just my opinion, I am not tax expert.
