Upvote:14
Pre-flight time limits are always based on the originally scheduled departure time, these include both check in close and arrive at the gate by times. The fact that a flight is delayed does not waive these time conditions, primarily because the airline will do what it can to get the flight to depart as close to scheduled departure as it can.
It sounds like your son made the mistake of assuming he could do as he pleases during the delay. This is never a good idea, because the revised departures times are "estimated" and may happen sooner than posted.
There is really no recourse other than writing a polite message, explaining what occurred and asking for their assistance. Maybe you will get a sympathetic ear, maybe not. But it sounds like the airline did nothing wrong based on the terms of your contract with them.