"ne comprends pas" means one thing, "ne...riens" another. This snippet, if accurate, says so much. It is a closure, a juncture of CRM. The flight is being re-set in the view of at least one pilot. I think the comment is within the boundaries of "Aviate," alone, not comms or Nav. No one would get to this point re: the mundane. Not even atrocious and frightening weather weather. The airplane is an unknown to him here, and shows a frustrated pilot partially into a situation with which he is greatly uncomfortable, and has no experience of. This moment is the initial onset of upset, or the immediate prelude. Again, if accurate, a year's worth of speculation coalesces into epiphane for all of us connected in any way with this tragedy. They are speaking to us.
Without context its difficult to say. If we were to only look at the four words presented, not knowing what preceded or followed, I'd "transform" this as "I don't get it!!". This sounds more like a verbalization of puzzlement (as in being confronted with contradictory information) than anything else. This is from my experience of living in France back in the day. Native French speakers may confirm or disagree with me. Its hard for me to read anything more into it (assuming the content of the leak is true).