Ex ground staff here.
Unless you noticed that there were two people with the same name, both ticketed on the flight, nothing would be suspicious.
If you saw two with the same name, you'd wonder what was going on and investigate but if it was a name like John Smith, it's not at all uncommon.
Throw something else in to the mix - what about thie scenario.
I don't know how EK's system works but if they used APIS data to look up the reservation - the Air NZ booking would not be loaded with it, as they've just provided EK with a list of names and said "fly these people on EKxx_ to YYY, we'll pay you later".
But the QF one probably would be loaded with APIS through the QFF profile etc - so you're doing the right thing, looking up a passenger by their passport information (remember, everyone's is unique) and checked in a passenger on a 100% ticketed fare. The passport number matches the booking, which matches the name, which DFAT have given an approval to uplift for.
What is incompetent about that scenario?