alt Hacker NewsHi! Author here. You're right — but two things to consider here.
First, that quote is referring to human-made systems, not natural ones (as is the rest of the essay!) and I think our views align on whether human systems regularly work.
Second, natural systems (and all complex-enough systems) are always running in some degraded fashion. So what "working" means is ambiguous: they are broken, yet accomplishing the goal. The quote from the essay refers to "working" in the "free of faults" sense, in which I again think our views align.
"they are broken, yet accomplishing the goal."
Are they really either of those two things? Natural systems have no "goal", they just are. If they change, they change. If they stay the same, they stay the same. Because there is no goal, there is no "broken". It is only we who assign some sort of meaning to them and characterize them as "working", either because they meet our needs, or just because we are inherently impressed by complex systems.