I've seen it too, and it really hits you when you see it for yourself.  It doesn't make any sense.  The Oliver Stone film makes the point very well by saying that the reason was to put Kennedy in a position where he could be fired upon from multiple locations, or as they called it, a "turkey shoot." 

This was a good article.  If it's true that the amount of lead missing from the bullet found on the stretcher cannot account for the lead fragments found which are supposed to have come from that bullet, then that pretty much means that there had to have been more than two bullets which hit the target(s).