...Actually they aren't big holes. Bones is starting master and control his distance, reach & timing. Not to mention his unstoppable ground n' pound. Jon over-commits with his spinning elbows and all but maintains the distance control and sticks to the gameplan. You get inside, Jon rips elbows. He's faced a little adversity and pulled through. Vitor's wicked armbar and Lyoto's bodykick is about it. Jon's frontleg sidekicks are wicked. They have a nice snap on them. Great technique. More effective and powerful than Machida's. Lyoto must have forgotten about eating his own medicine by getting dropped with a big straight left by Jones. That was the beginning of a quick end for Lyoto. Once Bones is in top position, he is so completely dominant. His slicing elbows and punches have so much leverage. Trying to figure out those holes is the question of the day.
Food for thought: Since leverage is one of Jon's key attributes, I bet if Stephan Struve locked in a super-tight armbar like Vitor did, Jon would have been submitted.