One of my professors had a letter writer who didn't submit an letter of recommendation to Berkeley till well after the deadline. These were the days before applications were done over the internet.
Berkeley wrote to him saying that they hadn't received one of his LORs. Since this was done via snail mail, he obviously only received the letter well after the application deadline. He was eventually still admitted. In fact, he decided to do his PhD there.
It's important to note that Berkeley did that despite the large costs (in time, at least) associated with notifying candidates of missing materials. So given that communication can be conducted much more efficiently today, there's no reason why they wouldn't do the same this time around.
So seriously guys and gals, if Berkeley says they will contact you regarding missing materials, they WILL contact you. Chill out.