The article is wrong about the regularity of the issue, the "weird control systems" (not sure what connection you're seeing with employee protection laws), and the causes.
But you misunderstand me if you think I'm burying my head in the sand. I don't deny that Whole Foods has issues with its ordering processes. In fact, I think the company has been going in the wrong direction there for a long time. The article is just so, so off-base - originally I didn't intend to argue with it, but now I've become this guy: https://xkcd.com/386/
It will be interesting to see if Amazon can improve the situation through automation. Generally I've seen stores that use automated ordering systems be far worse with their out-of-stocks (Kroger, for instance).