Some of the crew actually discuss at different times how many bad apples ended up in the initiative. That they should not have passed the screening process.
I think that secret collective area that you find isn't meant to be found. Or it is a mission that never triggered. There is a name associated with it. You never see this name until after the Sloane/Reyes pick. If you go back and look at Reyes, terminal/data pad, forgot what it is, it says he is to talk to this person. Think it starts with a L. This L person is who is responsible, maybe one of the dead body, don't remember in that secrect collective area.
The room with the dead bodies in cages was the cannibal crew. It is close to the secret collective area and one of the first side quests given to us on Kadara but it is not the Collective. Sloane's guy threw out someone who paid...