The first bunt served to move the runner to second. The second bunt would have been intended to move him to third. I wondered if they have observed that Hernandez is good at bunting toward third but not toward first. In other words, might the Sox have decided that 1) the Dodgers expected the bunt and 2) Hernandez might bunt it toward the third baseman so hard that he gets JBJ with a tag, or that a deadened ball makes it too easy for Martin, who is skillful enough to get jbj at third. Arod kept harping on the obviousness of the bunt there so I can't help wondering if the Genius had a good reason for not calling for it. I have a lot of respect for Cora, so I would love to know his reasoning. It was way too late to wait for his post-game remarks, so I have no idea if he addressed it.The last time they gave away an out on a bunt, they failed to score, so Cora probably decided to not make the same mistake twice. It would have actually been a shrewd move if JBJ had been paying attention to the path of the ball. He could have still made it to third if he'd taken off as soon as the defender committed to throwing the speedy Marco out at 1B, because he would have had to rush the throw.
That's my best guess.