I think the only cases of major system failures that could be blamed on human error, are ones where people INTENTIONALLY did wrong stuff, sadly, these cases do exist and were very lethal.
1. First nuclear accident: the theory is one operator was upset that another operator was screwing his wife, and removed the control rods 100% when he was scheduled to work on them, causing a sudden spike in temperature and then a water hammer that killed everyone in the building. (and made it JUMP!!!)
2. Chernobyl, although many people (specially anti-nuclear) blame the accident on the design, it was obvious deliberate error, even if the intentions weren't malicious, the operators ignored alarms, then DISABLED the alarms, and intentionally pushed the reactor past safety limits, even if it didn't had the design flaw it had, it was possible they would still find a way to blow it up if they kept their behaviour.
3. Depressed airline pilot, locked co-pilot out of the cockpit and crashed on the ground on purpose.
There are probably other situations out there... thing is, those are situations no matter how well the system is designed, it will still happen, it is impossible to make a "malicious-proof" system, after all, even a rock, with zero moving parts, can be used in the "wrong way" and kill someone.