Corrected entry: In his alternate "fiery vision," after the attack by Bane aboard the Logos, Neo delivers the final blow to Bane's head, so hard that the skull is completely severed from the body. Yet in the very next shot, when the camera returns to "normal vision" showing Neo standing above Bane's corpse on the ship's floor, the head is exactly where it's supposed to be, still firmly attached. There's no reason for his alternate vision to be that different from reality.
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Correction: His body also disintegrates into thin air before he hits the ground, so I'm guessing the decapitation is just a representation of his programming being destroyed, not the physical body.
Johny English