Whether the knee was legal or not isn't as important as the fact that the rule itself needs to go.
KnowKontrol - Second knee was to the chest.It seemed pretty clear it was to the chest
While I don't really want to see knees to the head ala Coleman/Goes from PRIDE days, the way the current rules are implemented need review.
Having just rewatched Vitor draw JBJ up out of his crouch with the threat of a head kick and Big John telling Jones,"If you're gonna play the game..." makes me think they need to do something to prevent flagrent manipulation of that gray area between being down and reaching for "base".