http://en.wikipedia.org/wiki/Moneyball:_The_Art_of_Winning_a...
One of the main reasons Jeremy Brown was featured so prominently in the book was because he was such a long shot to make the majors but was being drafted anyways. He was also doing pretty well in the farm system his first two seasons before injuring his thumb. It's sports - lots of players, regardless of how promising or hyped they are, have to leave the game for a wide range of reasons. Jeremy Brown's career is not at all evidence that Moneyball's premise was flawed.
Sabermetrics isn't clairvoyance. No matter how good your data, you still have to play the game.
Meanwhile, while we're playing the anecdotal-data game, those of us in Boston are pretty happy with Billy Beane and company's predictions about Kevin Youkilis.
It's one thing to point out that, having identified and (famously) exploited market inefficiencies in the MLB Draft, Billy Beane helped eliminate his claimed edge. That's how markets work. It's another thing to take Michael Lewis' book, look at the career of one of the central characters (Jeremy Brown), and find that he wound up only getting 10 at-bats before retiring. Ouch.