I'd say the upgrade system somehow caused a double issue of those boarding passes. It sort of makes sense, removing you from the seats was to reduce the embarassment once QF determined someone else had BPs with the same seat numbers and were likely revenue passengers so suddenly they became priority.
If that's what happened, surely modern flight res systems don't do this? That's one hell of a screw up... I'd be milking this for points.
Speaking of modern flight reservation systems, haha... Something similar happened to me on AA a few years back
I had an overnight planned in NYC, but due to issues that day with late flights and missed connections, I ended up in Boston overnight instead. The BOS station manager gave me the details for a hotel where AA would pay for me to stay that night, and to make things easy the next day, he also checked me in and printed my BP for my departures the following morning (to save me time when I came back the next day).
So, the next day I arrive at BOS; through TSA security with my BP no problems, into the Admirals Club with my BP no problems, get to the gate and my BP doesn't work! Gate agent tells me there is someone else allocated to my (paid domestic first class) seat. Luckliy the other passenger hadn't boarded yet, so the gate agent asks me to stand aside while she investigates.
Turns out, even though the station manager had checked me in to the flight the day before, the system had automatically cancelled my ticket overnight, and an EXP had been given an upgrade into my seat that morning, as it was then showing as empty in their system.
Anyway, a massive amounts of typing into the computer later, and I am back in the seat which I paid for. Then one angry EXP was paged and told his upgrade had been cancelled, and was issued a new boarding pass for main cabin. All sorts of
dissatisfaction comments coming out of his mouth.
So, yes, I am going with potential system failure somewhere too.
I have also been kicked out of a domestic upgrade seat on QF before, and at the gate too - by a pilot, but at least he was in uniform, and then spent the flight working on paperwork.