Nothing necessarily went wrong depending on your world view, humanity as a whole was likely better off under Prometheus. But, if you do not relish life under the guidance of a nearly omniscient AI, then the place the Omega Group went wrong was both not realizing that they were being manipulated and not realizing that they were a break in the boxing.
They were the medium that allowed Prometheus to influence the world in the ways that they were afraid. I am still not sure if the story ends more utopian or dystopian, there was more peace and prosperity for more people but there was less human input in human civilization’s direction. Sure there was less species wide free will but living today there’s still limits to the actions an individual can take, my free will is already limited. We would simply be moving control from governmental humans to a more networked AI. Each has the potential for doom and destruction, so from an individual’s lower viewpoint there may not be much difference.