Mission Control basically organizes/manages your application and it's windows so you don't have windows everywhere (like it was in Leopard/Snow Leopard) and allows access to them. It does what it's advertised to do, what's the problem you're having?
EDIT: I see what you're saying. You don't mean the ACTUAL desktop but the desktop spaces. That's not suppose to happen, the windows are suppose to be centred below the spaces. This was happening to some people. Does it happen to you all the time? As of right now, there is no fix - you'll have to wait for Apple to acknowledge/address this.