Well, one of the reasons is that a lot of systems theory was basically trying to apply notions, concepts and mathematical analysis from physics, firm management

Well, one of the reasons is that a lot of systems theory was basically trying to apply notions, concepts and mathematical analysis from physics, firm management, and game theory to contexts where they just didn't apply: ideal rationality of agents, information flow diagrams, and even notions like equilibria. The notion of equilibrium in ecosystems, for example, came from the physics of gases in vacuum chambers, neither organisms or populations of organisms exhibit such tendencies. There are many more examples of why mechanistic explanations simply don't work for many phenomena in the philosophy of science. Weiner, Simon, and others were just trying to use the maths they knew to solve some bigger more complex problems and in the process ended up stretching the metaphor of the system a bit too far.