Technically, there may be absolutely nothing wrong with the young pilot.
Twice, maybe three times in my life, I have experienced a strange experience upon waking - almost like sensing another reality for a second or two. It was fascinating.
I mentioned this to my appropriately qualified son, who said there was quite a lot of research carried out on those few moments between sleep and being fully awake.
This is almost certainly because of that momentary window into another mode of brain function is so out of the ordinary.
The pilot had seemingly enjoyed a long sleep. Perhaps tiredness caused it to be a very deep sleep. Such a shame if this ruins his career, when the effort should be towards making the aircraft safe from such sudden and unwanted inputs.