There is also likely a human error component. When you make someone manually scan 150 people they stop paying attention. They should have some kind of error message, but if it looks like other error messages (like the ask about emergency exit message), it's possible the human confused the error and cleared it.
The shared gate agent computers are built from an industry-standard OS image (8 years or so ago this was Windows XP SP2, and not SP3, never SP3).
Don't just beep the same way every scan beeps, make a different noise. Show a large red "STOP" sign on the screen along with the problem.
When you need to alert a human to an event that only happens once in every few hundred cases, you can't be subtle.
Bingo. This is not really a job that people, in general, are any good at. If there was an automated turnstile that didn't suck, that'd be a great place for one, so they could focus on the exceptional cases instead of being lulled to sleep by the happy path.