I don't think it's in any way a 'mistake' - they bought an aircraft which, at the time, and for a couple of years after initial delivery, performed perfectly adequately on their long-range routes to LAX.
I think this issue really has nothing to do with Qantas and their choice to operate the A380: surely you could easily brand this as 'Airbus' mistake' having chosen to power the A380 with the Trent 900, considering this engine is supposed to scale to 80,000+ lbs of thrust (for the 380-900) but can't even supply 72,000 reliably?