Almost certainly human error.

Anecdotally, I had a standby ticket recently when my seat was reassigned to a paying customer, although I still had a boarding pass for that seat. I was halfway down the jet bridge before the gate agent realized that my ticket had been revoked.

I imagine it's second nature for gate agents to let passengers through, and one lapse in judgement can cause the United incident, despite the software showing that the ticket was invalid.