I’ve absolutely had this problem, and possibly one step worse. Lodged a claim for a JQ flight taken in March, eventually received SCs at the end of May after calling a number of times. Then, randomly at the end of July the same flight appeared on my statement as “cancelled” and the SCs were deducted!! Made another call to Qantas and was told that they didn’t have adequate substantiation and I’d need to send through my BP. No explanation as to why they were credited then cancelled! Sent required substantiation and received a strange email from service centre stating
“I've reviewed your membership, and i can confirm that the Qantas Points and Status credits accrued on the flight was not cancelled nor deducted.” - when a screen shot of my account clearly show they were! Again I called Qantas and went through things again, and was asked to send substantiation again...
Mysteriously, three days later the points/SCs were reinstated without explanation.
In an even stranger turn of events, I received an email from Qantas approximately six weeks later (end of September) to advise that the points had been credited! Truly bizarre!