Ali Bin Somewhere, well I am very sorry to hear about QR (but somehow it doesn't surprise me) not complying with the instructions, given by you. To answer your question: Your issued instructions are a MUST and nothing else and if not able to comply a pilot must inform ATC. Anything else is pure unprofessionalism. In my opinion you guys should treat it accordinly and inform the airline, which hopefully will take appropriate action.
Cheers.