I don't have a 2012, but the suspension problems I've experienced with my 2010 SES (purchased new) are spot-on similar to the ones you folks are experiencing with your MY 2012s: a noticeable clunk/knocking noise when travelling over broken pavement/bumps at low speeds as well as an incredibly annoying squeaky metal-on-metal scraping sound when backing out of the garage or entering parking lots/driving over pavement seams and approaches. This all started when the car had just a couple thousand miles on the clock and has been aggravatingly omnipresent ever since. Interestingly, it's always rattled like a tractor right at start-up (I used to believe a loose exhaust component was the culprit) which leads me to believe there's some creedence to the theory of motor mount(s) being an often likely cause of these noises.
Unfortunately, due to a couple of recent moves and having a very limited amount of uncommitted vacation time after purchasing the car, I never had the opportunity to bring it in to a service dept. to address the issue(s) until very recently (it helps that I currently reside within walking distance of the local Ford dealer). With the factory warranty now expiring in less than a year/6K miles, getting Squeaky (aka SirClunksalot) fixed is now becoming a more urgent priority.
Ugh. What a pain. I picked up the car this evening (3rd service visit for the same problem - the only parts replaced at this point have been the sway bar links) and the dealer is now pivoting from a "we can hear it; we just have to figure out what's causing it" stance to a "it's normal; they all make that noise" position. Yeah, right! If it was normal, they all WOULD make that noise. So now I have to start going up the ladder.
Ironically, I was seriously considering replacing this vehicle with a MY 2013 Fusion later this year (I realized the Focus was too small for my needs almost immediately after buying it
). That consideration is quickly fading. Ford has about 5750 miles to get this solved or when I go to trade it [before the warranty expires], it won't be for another Ford product.
Keep on 'em and good luck, folks.