In regards to QF this is not the first time this has happened, maybe just the first time the ATSB has reported it.
This goes back to when the Amadeus Flight Management system was implemented. It was overcome by training the people who looked after the group check-in to recognize this and it was sorted out during the check-in process.
My theory as to why this may have happened is to do with the staffing levels at airports, being that they have to do more with less. If it was someone who doesn't normally do group check-in they may not have been aware of this.
I've got no doubt that unfortunately this will occur again at some time in the future.