score:3
From the posting dates ("Dates" on your pasted data), it would appear that they neglected to post your wife's flights right after your travel. Then when they did post them, they posted them as full fares rather than discounted.
The full fare points could be a gesture of apology for the delay in posting, a result of them being unable to determine the original fare class or simply a mistake.
For the missing flights, you will likely need to send Qantas copies of her boarding passes for the return flights. Boarding passes are the only real proof you checked in. Of course, the downside, is that armed with boarding passes and ticket number, they may realize the outbound flight was credited wrong and adjust those points down to the same level as yours.