They're not saying that automation doesn't reduce accidents. They are saying that the accidents that occur now are sometimes caused by the human operators becoming deskilled because of the automation.
When you say:
" ... it's just something as simple
as a proper error reporting system."
you make it clear that you don't work in automated real-time systems. I do, and it's more complex than you seem to think.
I know of a case similar to the grounding of the Royal Majesty. In that case, again, the GPS antenna became disconnected. There was a proper error reporting procedure that was defined and documented, and yet still no one fixed the antenna, and still everyone trusted the AIS/GPS system even though it was reporting as broken. In the same way that Windows users are "trained" to click "OK" on every pop-up dialog, so they were "trained" by their day-in, day-out experience to trust the system even though they'd been told it was broken.
You also say:
Debugging and testing is important.
I don't think there would be many who would disagree with you, but are you suggesting that the systems described had had no debugging or testing? Of course not. They had been debugged and tested. Exhaustively. And knowing something of the field, most likely rather more than you imagine.
Bugs remain, and when they surface, humans need to be able to take over swiftly and accurately. Increasing automation makes it less likely that they do so. Even if you've had extensive and intensive training, if you don't use it for six months then you are unlikely to remember it all in an emergency.
That's the message of the article, and I endorse it, because I personally have seen it happening.