I saw that play. In HS rules, once the ball breaks the plane of the goal line, it is a touchback, but in NCAA rules, the ball can be brought out. According to the officials in this game, the ball never broke the plane coming out, so it was a touchback. Personally, I don't see how that is possible - he stepped out of the endzone pretty good. If the player would have brought the ball out and then went back in, it is a safety. Whether it is a safety or touchback depends on who put the ball in the endzone.
What I think happened is the play caught the officials by surprise and they ruled like they did. JMHO.