Has anyone ever had a problem with their oneworld ticket while using that ticket?

I'm currently on a DONE3. Sitting at HEL for HEL-LHR. Booking on AY with an MH code. When attempting to check in, that sector, and only that sector presented problems. They couldn't find it under the normal ways of looking up tickets (name, passport, PNR) and could only find it when imputing the full ticket number. It took almost an hour and 5 different agents to get it worked out.

It seems that MH cancelled the sector and it was showing to AY as waitlisted.

I've had some other problems in the past, but those have been a result of a clueless agent changing something they shouldn't have when making changes to other flights or connecting across tickets.