The emergence of mutants and supernatural abilities didn't lead to global chaos thanks to the all-powerful World Government. The over 60% mutants populace has to follow the laws just like the rest of the populace which consisted of ordinary humans; resulting in a stable world and development that gave further rise to technological advancement. The only exception being the forbidden regions and Lizenea where the government didn't have its hold.
In civil society though, there were strict rules on what type of mutant could use their abilities in what place and situation; with certain exceptions like defending oneself and so on. The rules weren't overly strict nor there were too many restrictions that ensured mutants weren't frustrated and give rise to thoughts of rebellion.
So, in short, the iron-clad law & order situation ensured that mutants didn't use their abilities as they please and thus, saving civil society from chaos.