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

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.