> Okay, but is there something particularly wise about getting an alert that a boarding pass has already been used and presuming it must be a glitch?

Did the gate agent do any follow up verification? Like checking the flagged passenger's ID?

In retrospect, modern computer systems are inscrutable and unreliable enough (as a category) that it's rational to disregard them, especially if you've done some independent verification. Rational doesn't always mean correct in a specific case.