Just sharing my experience when I had the exact same issue during the Xmas holidays flying WY. Aeroplan award booking made in Feb. 2025 for travel in WY from MCT - DOH 2x pax in Business on 1 Jan 2026. I had flown MEL - SIN (SQ) - KUL (SQ) - MCT (WY) the week prior with no issues at all during check-in at MEL.

I tried to check in via the app for this flight and the exact error message appeared so we decided we'll just check in at the airport.

However, at MCT, the check-in agent initially couldn't find the booking and then kept furiously typing something on the keyboard and kept staring at the screen and sighing and had to call someone to assist. She explained to me that there is something wrong with the booking and asked if I ever changed flights etc. which I hadn't. An hour went by, we were still in the check-in area (at least there were comfy couches in the Business check-in area at MCT) she approached us and said her shift has finished but assured us she has done a handover to another colleague who is sorting this issue for us.

About 30 minutes passed, the other colleague asked us what the issue was (WTH !!) I was miffed to say the least and asked him to go speak to his supervisor who had "assisted" the previous agent. He then made some frantic phone calls (everything in Arabic so we had no clue what was going on). After about 2 hours, he informed us that he figured out what the problem was. There was a duplicate PNR for my partner travelling in this booking and so he now needs to cancel the dupe booking...that took an additional 30 minutes and eventually we were on our way but that meant very little time in the lounge.

The only saving grace was the lovely FA on this short flight who happily kept topping up our champagne glasses.