The title of the article is an intentional conflation of "systems thinking" with "magical thinking", which is not a compliment.

Couldn't one interpret "magical systems thinking" as a fallacy that people may commit when applying systems thinking? More broadly, I find some of the comments here rather harsh, also considering that many observations in the article are intuitively true for anyone whose ever been exposed to bureaucracy on the meta-level.

One could interpret the title that way, but not consistently with the rest of the article, which includes assertions like "in the realm of societies, governments and economies, systems thinking becomes a liability".

I think there's plenty to agree with in the article's descriptions of failure and hubris. What the critical commenters are taking issue with is that the article blames those symptoms on a straw man. It's a persuasive article, not a historical review, so it's reasonable to debate its conclusion and reasoning as well as its supporting evidence.

Exactly, it's a fallacy of systems thinking but it's not intrinsic to it. In fact, system thinkers tend to understand that complex systems, are, well, complex and not easy to reason about.