When I say that I've "seen" it, I mean that it has happened quite a bit when I've been on the field. I'm not directly watching that as my main focus at the snap of the ball is on my keys to the outside of the formation. So if the way that I worded my post came off wrong, I apologize. With that said, I do see the snap go over the QB or up backs head. Any official can tell you that they see a lot of things beyond what they are focusing on. Having a good and wide field of vision is very important and allows you to notice a lot of what's going on. Having "tunnel vision" for only the one specific thing on which your eyes are focused is a bad thing. If I'm watching a split end coming off the line, I can see the snap and the ball out of my peripheral vision.
Also, our crew brings a blank DVD and pre-paid postage to every game. About half of the time, the coaches are kind enough to provide us with a copy of their game film, which we then study so that we can try to get better at what we're doing. A lot of the time, that is when I catch the "bigger picture" of the play that's going on outside of my particular responsibilities.