I couldn't agree more. I've lost count of the number of times I've explicitly said to an agent 'Please completely remove the X FF number and insert only the Y FF number' only to check online myself and find them both in there. It's lazy or it's incompetence. Either way it shouldn't happen.
This probably happens because when you add a QFF number on the QF site, it adds it without a segment association which means it applies to all flights on that PNR. When they add your other FF number, the system most likely adds it as a segment associated entry (associated to that specific flight). Therefore that's why you'll see both.
For you to picture what happens, this is likely what it looks like in a PNR, after the lounge has changed the FF number:
SSR FQTV QF HK/ QFxx_xx_x
SSR FQTV QF HK/ AAxx_xx_x/S3
Where the first SSR is the 'all flights' FF number and the second SSR is the specific flight associated one. S3 being the flight it applies to.
You could probably get around this issue by having your QFF number specifically assigned to each and every flight so that there's no "all flights" FF number SSR in the PNR. The QF site won't let you do this however. You'd need to call up.
Example:
SSR FQTV QF HK/ QFxx_xx_x/S2
SSR FQTV QF HK/ QFxx_xx_x/S3 (changing this to AA when appropriate)
SSR FQTV QF HK/ QFxx_xx_x/S4
SSR FQTV QF HK/ QFxx_xx_x/S5
CX's site in contrast lets you do this on CX flights without any issue. In fact everything you do on CX's MMB defaults to be strictly segment associated.