I don't know if I'd chalk it up to agents ignoring error prompts. Some passengers manage to render their bar codes unreadable between issue and boarding. I'm guilty of this myself. I set my drink on it, or fold it, or otherwise funk it all up. So I get to the boarding agent, they try to scan it, it doesnt work, so they just "on" me manually by seat number. Hence no prompt until the "real" passengers boarding pass scans and the prompt goes up that they are already on. Agent checks to make sure that indeed this is the correct passenger, and lets them go...but I'm already in the seat.

You could theoretically make it harder to "on" manually. Perhaps by seat number AND last name...but I wouldn't guess it happens often enough to slow down the entire process to protect the occasional passenger who manages to board the wrong flight