• In one mission, you have to detain a corrupt FISA (= FBI) agent - he may pull out a gun and shoot you, if he feels like he can take you out.
• You have to raid a house where three brothers are illegally modding and selling guns, to pay for their mother’s cancer treatment. She tipped off the cops, to stop her children from getting into too much trouble; if you end up using lethal force, you’re killing the sons of a mother who believed in you in front of her, and the game doesn’t count that as a failure.
• There’s an in-universe equivalent of MKUltra, and the main character is apparently a successful test subject of it. Some speculate that the USIA (= CIA) is artificially facilitating crime in Los Suenos to put you to the test.
• A mission briefing states that a police officer (or many? idr) beats up a detained suspect, who has to be sent to a hospital - the “victim” did massacre an entire night club with his buddies, but still, it’s technically police brutality.
• In the last mission of the base game you find a cargo container with human trafficking victims in it, then a sus conversation happens where another FISA agent butts in the comms and orders you to close it; it’s unclear what’s going on, the entire game teaches you that it’s specifically not your job to take care of injured civilians and whatnot, but the tone of the characters implies that the FISA agent may be trying to cover the tracks of the criminal organization.

MKUltra.