A lot of people (myself included, hence why I looked up how to fix it) have found that they can't use their mouse or keyboard when they first get into COOP mode. The fix is really weird, but I promise I'm not kidding.
Hit Alt+Tab
Hit Alt+F4
People are saying (maybe just educated guessing) that there's a program that tries to run over the game, so your commands go to the mini program rather than the game. This fix shuts that down and brings your commands back to BF3.
Hope the next patch corrects this, but you never know.