in the manga, it definetely shows that he hits 64 times and not 126. Also, most of the scanslations say that Neji hit "64 tenketsu", not "all 64 tenketsu". Of course it's impossible to hit all, the one he pressed on Hinata was at the back of her arm, he would have to stand behind naruto to press it. So we can assume that he didn't press all of them, just enough to make him stop moving.