I would disagree with that. The boarding ID had been used once and can't (shouldn't) be used twice. In that case the first use was in error but the system can't know that. So the correct course of action would be to re-check everyone's boarding pass. That may have been impractical / undesirable, but simply ignoring the error as a bug seems careless.

Maybe if flight attendants were actually getting paid while passengers are boarding they might be more attentive

I don't think their checks caught him though? He only got caught because the plane was full, and he stood out like a sore thumb when he couldn't sit down somewhere.

If boarded still means "on the vehicle," both people boarded.

One person was a passenger and the other was a stowaway.