Needhimback,
It must have been really horrible to see your application in such a mess. I'd have been devastated too after spending so much time on it :'(
It might make you feel a bit better to think that they probably have a lot of admin or clerical staff checking off different elements of the application packages, separating them out and delegating work to those staff - so they'll probably have to be taken apart anyhow. Which is why you hear of people's papers getting lost (!)
We all send our files in looking really organised and well-presented because it means so much to us. Like you, i put my heart and soul in to our application.
Sadly, they won't have that emotional attachment to our papers; it's just another bundle of paperwork to them. (I often wonder how they'd feel if they were having to go through this process and having to put their lives in someone else's hands, so to speak).
I hope you don't get anything else sent back to you, good luck!