that's what this was.

Someone noticed the missing tattoos in the media guide and asked BYU if they touch up photos of athletes. Of course BYU touches up photos--they do it all the time. Various little things need tweaking in most photos before they are suitable for publication. So they said "yes, we do", and that was all the reported needed to run a big expose on the Rafa tattoo-gate.

Except they hadn't touched up his photo to remove any tattoos. Like you said, those photos were from his first season at BYU, before he got the tats in question.

It's really pretty hilarious that so many people were so outraged by that. And pathetic (since it didn't actually happen).