The lede reads, verbatim: "The computer failure that prompted a halt of all US flight departures was caused when a data file was damaged as a result of a failure to follow government procedures, the Federal Aviation Administration said Thursday."

It is clearly implied that had the rules been followed, the corruption wouldn't have occurred.

Your blame-the-FAA scenario where the rules were incomplete or flawed isn't ruled out, but I don't see value in asserting it without evidence. I think it's perfectly plausible that someone just cheated a bit. That's hardly a rare situation in any IT environment, and so it seems like Occam favors the article's interpretation.