Sounds odd, as you suggested usually they only auto lock when in motion, unless the immobiliser auto lock kicked in, but you said the engine was still running.
I have a faulty/intermittent RHS door switch on the Prado. If I open that door and don't open any other door, it will auto lock as it doesn't detect a door has been opened.
If there was no auto unlock and he left the vehicle running, I wonder if the immobiliser kicked in and relocked the vehicle after the door was opened?