It's not really a security breech as there is no security when boarding the plane. All that's happening when you board is the airline is making sure you have paid and have permission to board. The boarding pass is really just revenue protection for the airline and a way to see who got on the plane. Maybe they never scanned his boarding pass. Maybe the GA was distracted for a moment and he walked on. There are a few ways he could have got on with or without his pass being scanned. Presumably the flight wasn't full and no one else had the seat he was sitting in.

Do they do headcounts on all flights? I really don't know but if they do then it should have been caught then. In the end it cost Delta to fly him on two TATL flights for no charge however as he was ticketed to fly a flight on Delta anyway, why would he be a security risk on one flight but not another?