I can imagine that the flight must have been still showing in the reservation system otherwise passengers could not have been booked on it.
On the issue of passengers are being told that the flights were full. Could this have being the case of a PNL (Passengers Names) being loaded into the flight hence showing the flights were booked full however some passengers may have allready made the long journey home or choosen another flight.
On many cases the website was the only way for passengers to gain information as i can imagine there was an extremely long waiting time to get through to the call centre for all airlines.