On Sherdog.com they are all saying Penn broke a rib late in the 2nd which is why he got beat in the 3rd, it would explain why his hands were so low in the 3rd...to protect his body.
As for GSP's comments, he only did that to sell his fight, you can tell it was not like him to say something like that, almost like it was scripted. He was very upset that Matt got upset about it and was very appologetic about it, Rogan said after the fight that GSP is a really nice guy and that it was clear he was trying to use American salesmanship to sell more PPV buys for his fight with Hughes. Perhaps GSP was trying to be like Ortiz to stir the pot, but he's too nice of a guy to make it work.