...there was one sound that actually irritated me and scared me once you heard it, and that was the noise that you kept hearing at the prisoner facility, that really low pitched "nnnnnnnnnnnnngggggggg" like two steel girders rubbing on eachother.
That I can offer some insight on, the movie used a lot of LFO. It's basically a warble/wobble sound, but often done very deep for a foundation with a higher pitch warble on top. A lot of the noises the 'machines' make are LFO based.
*edit* I realized that was a great description ...so...
LFO for low-frequency oscillation. It's usually used with sub-bass sine waves, then an octave up, LFO to give the bass depth and unease, and the in the mid-bass the gritty, terrible saw waves with a bunch of LFO. In music the electronic producers figured out in the 70s and 80s that just bass doesn't really have enough depth and sounds very similar, so layering LFO on top gives it individuality and personality. More recently, drum and bass and dubstep producers started using a ton of it, and now I've started seeing it in movies more often. The right combination of LFO with sub-bass can make people very uneasy at high volumes.
Check this song out, listen to the bass:
0:34, 0:47 ...you can hear it really good at 0:53 ... listen the the pulsating of the bass. This is a bit lower frequency than the movie uses, but you can hear how when the frequency is raised it starts to sound like the machines and a lot of the sounds they used in that movie.
This tune has a lot of LFO also:
Hear what I mean?
Is that the sort of sounds you are talking about?