That corresponds with what I've seen about it: nobody ran a stop signal, since there wasn't one as explained by Jersey Mike. One question is why the conductor, who was on the leading end, and was or should have been in communication with the engineer on the engine at the rear, didn't have the train stopped to report that the crew was not qualified to proceed further. I believe it's standard practice, if a train or engine crew is directed to proceed into territory where they're not qualified, to inform the dispatcher of that fact. (As it was, they had to wait for a qualified person to get out there to act as a pilot to get them back to home territory.) Since there were no fatalities, injuries, or damage to equipment, this may be simply an internal investigation not involving the FRA; there may be no telling how much of what transpires in the investigation will be made public.
(By the way, that second photo is a rarity: a low-level bracket signal comprising two dwarfs, governing respectively the left- and right-hand tracks.)