ok, taking a guess here and others can shoot me down on this.
I am guessing that there was an obstruction in the primer hole when this round was reloaded and that is why you were seeing the primer slightly extended above the lip.
When you pulled the trigger, the primer went off ( it would sound like a small pop though) and what you felt on your cheek was the charge blowing back through the bolt body. The obsturction kept the powder from igniting and the primer discharge would go through the firing pin hole. Seeing all that carbon on the bolt head is what leads me to think that is what happened.
The primer discharge is what forced the extractor out of its normal position, but still in the bolt head, and when you drew the bolt back, the extractor, pin and spring then fell out, along with the round.
That is what makes the most sense to me from what you are describing.
Only other time I had heard of this happening was on factory rounds where they forgot to drill out the primer hole in the round. That was in a Remington action and it only forced the firing pin out of its normal position after the trigger was pulled due to the discharge through the bolt body.
The ammo in this case was federal, and out of that box of 20 rounds, the op found a total of 3 that the primer hole had not been drilled through the brass.