Sent from pillar to post only to miss flight

I booked a flight for my employee. He arrived early enough (and without check-in luggage) to just check in at the self-service machine. When he did so, the machine told him to go to the ticket counter for assistance, which he did. Once there (after queuing for some time) he was told to go directly to the check-in counter. He stood in the queue for around 30 minutes (without any boarding call announcements being made form the check-in counter personnel), and when he got to the front of the queue, he was told that he was too late to check in. He tried to get onto another flight but was told he needed to pay full fare. I called and reported to Lorraine but was told unsympathetically that he was simply too late.