I kind of replied to this in another post just now about some of the scripted sequences in the game and how they behave and why. But as for normal encounters (like the one you mentioned), we might make an area where when you walk in 3 guys walk a patrol and come around a corner. Now how you handle it is up to you. If you go in guns blazing, all three are going to turn on you, and in some cases a guy might break off and go get some re-inforcements. If you are sneaky and sneak up closer to them to take them out quickly, perhaps nobody else in the vicinity will have noticed. If you're in a heavily populated base, and you decided to kill them in an area that was open to others, they might see you kill them and start other events happening.
So, it's not scripted in the sense that there is only one way to do things and the same thing will happen in every case all throughout the game. Some cases are like that, a lot are not and are more open ended as to what the AI might do, and to how you react.
------------------
-----------------------
Latuh fuh U,
Benson
benson@2015.com
"We don't introduce or cause bugs in the game, we merely find and bring to light the inadequacies within the code."
-regarding level designers