I was wondering exactly this, how is it possible to use a boarding pass twice. The answer is, "the agent assumed it was a glitch".
It's interesting that we use machines, and when they flag the type of error they were designed to identify, we simply assume they don't work. Many plane accidents happen for a similar reason, the pilots thinking the systems on board are wrong and they're right.
Why don't we trust the machines? Is it because they have bugs and are sometimes actually wrong? Or because we trust our feelings more?
If the checking had been on paper, with the agent simply ticking off a list of passengers at the gate, would they have made the same mistake and assumed they got it wrong? What if the list had been ticked off before by somebody else?