This happened to me recently where I applied a SWU on the international sector that was waitlisted (in the end didn't clear). In the morning for my domestic flight I noticed I was not on the upgrade list and they manually added me at the airport. Even in the app it showed my status as requested, but I wasn't on the list or on the T-4 upgrade list.
Not sure if the SWU waitlist caused a burp of some sort or if the EXP agent was supposed to re-add me to the complimentary waitlist after applying the SWU. I am not 100% sure.
Based on the frequency of this kind of post (there were several others reporting similar issue in recent months) appearing lately this is a small concern and I hope this issue doesn't become more frequent. We just need to be a little more proactive and check the upgrade list on the app at T-4.