The crash in Japan is actually an example of a failure that fits the Swiss Cheese model. I think ultimately most of the blame will fall on the surviving coastguard captain, but everyone involved had a chance to stop that crash. The coastguard messed up and joined the runway when he shouldn't have. Mistake 1. ATC didn't notice the warning on the monitor that would have drawn attention to this. Mistake 2. The pilots didn't see the coastguard plane on the runway. Now, this one, is a tough one. With all the bigger planes with beacon/nav/interior lights, the runway lights, the airport lighting. It may well have been hard to see the small plane on the runway, but it had beacon lights on, and they had the opportunity to see it and abort the landing.

So essentially there were three chances to stop that accident and all three were missed.

I completely agree, designing a feature on a plane that doesn't respect this way of thinking is not the behaviour of a responsible aviation company.