The 23 years I spent in the Marine Corps as a 2600 as a starter. The 20 years my wife spent in the Marine Corps also as a 2600, as a second opinion on the matter. He might have gotten yelled at but he wasnt NJP'd. Classified documents are stored and accessed in secure spaces. Having a classified document on his desk and leaving it there while he went to the head wouldnt violate any security regulation. At worst he violated some weird local rule, but that wouldnt rise to the level of NJP.
Good enough?