An issue that I have encountered in the past (not unique to Qantas BTW) is when trying to book 2 people travelling together but each with separate frequent flyer numbers and/or separate credit cards. In all attempts so far this has required 2 separate bookings. Unless I am missing something, there does not seem to be provision to allow 2 travellers to book and pay separately within the same reservation request.
Maybe not a huge issue for most, but annoying to some.