He/she didn't say "What do you think you are doing?" though. Which would have been over brusque...
I understand the question to mean "don't tell me what heading you should be flying, or what you estimate to be your heading corrected for the system failure - tell me what the erroneous reading is". After all, knowing how much difference there was between the actual and their picture of the world would be useful information - if the answer had been actual +/- 180, that's almost a diagnosis of the problem in itself. When you are debugging something, what you need to know is *how* it breaks, not just that it's broken, and this goes for any problem-solving.
But then, I'm a native English speaker, and it does sound quite a lot like "What do you THINK you're DOING?"