I am trying to understand how your situation is an "excess HSA contribution". Did you or your employer contribute dollars to your HSA in 2016? Was that amount in excess of the annual limit ($3350 or $6750 in 2016 - done from memory)? If not, you probably did not have an excess contribution.
What it sounds like is that you had a "mistaken distribution", that is, you took money out of the HSA which you did not mean to (because you weren't supposed to pay for it anyway). In this case, the proper procedure would have been to contact the HSA administrator, report a mistaken distribution, fill out a form, and send the check (from wherever you got it - the medical office?) to the HSA administrator. That would have been the end of it.
However, now you have asked for the return of excess contributions (when I don't think there were any), and worse, did not do it until several weeks after the due date of the return. Did you file an extension for 2016? If you did, then you would have had until October 2017 to withdraw the excess...except that there was no excess.
What to do now? You did receive a check for $135, right? And you sent it to the HSA which you thought made for an excess contribution, right? I suggest that you call the HSA and say that there was a misunderstanding (at least on your part) and that that check should have been part of a mistaken distribution, not a contribution at all.
While they probably can't/won't go back and fix the 2016 paperowrk, you may discover that this is what they thought all along, which would solve your problem.
You asked for the $135 to be sent to you, right? And it was sent in May, 2017, right? And you got the 1099-SA for this in early 2018, right? Was the distribution code for this '1' or '2'? Furthermore, was this $135 lumped in with other distributions that you made for qualified medical expenses in 2017?
Before I go any farther, let me step back and see if this describes your situation...
