Pax have handed me both wrongly pulled coupons and also incorrect boarding cards at check in and when boarding a flight. This seems to happen a lot more during holiday season and I can see how easy it is for someone under pressure to clear queues to accidentally pull the wrong coupon/check in the wrong person/wrong flight/throughcheck baggage on a connecting flight when there is in fact a stopover. I've come close on a few occassions myself.
However, this is usually picked up on and I can't see how someone would use this "loophole", if you can even call it that, to get round security. It isn't common place, and is obviously unpredictable as to when it occurs. I wouldn't be screaming about security breaches on this one. As many others have said here, there are far greater problems.