I'm not saying that this is the captains fault, of course he is in charge and has full responsibility BUT there must be a "system error" when procedures doesn't work...
As far as I know the civilian airbus was listening to the emergency frequency but since no identification was broadcasted like a transponder id, just a heading and a speed indication which in this case was 65 knots faster than the max airspeed of the aircraft that time...
There were a series of events which caused the shoot down, BUT again, why didn't anyone doublecheck the information. The radar control officer thought that he saw the aircraft descending when infact it was ascending, this was confirmed by the warships computer loggs... if someone would have double checked this info, those people onboard the aircraft would have survived the day and the captain would probably still be a captain today...