No, this is not really a problem. What is the problem is how KM managed the implementation of their new policy. A simple announcement at the gate, preferably including a reason for the change, could have avoided this.
Too often passengers are confronted with inconsistent and changing procedures that they must follow. Is it so difficult letting them know what's expected of them?
I also see it as being a problem that despite the billions spent on airline and security systems that it is still possible for a passenger to board the wrong aircraft. A manual check at the door, which doesn't always work, shouldn't be the solution to this real problem.