The Pepe tackle was a red. I've referees only issue a yellow for it before, but most of the time those sort of challenges see red. Barca has seen a fair amount of refereeing help in the various competitions they play, but in this case alone, the correct call was made.
It was reddish because the studs were high, but he went for the ball (that was his aim, even if he was very late), so I get why its viewed as slightly harsh, mainly because referees let shit like that slide too often (how career ending injuries happen) and we gotten used to it, makes bit more orange then red because of it (mainly EPL refs). Its justiable to call it red because it was recklessly high and studs (see below pic), but I could have understood it if it was given yellow in another scenario (despite Pepe deserving punishment for his reckless stupidity), but in general high stud tackles like that shouldnt be allowed to fly (couple inches lower and Alves knee would been goner).
But what made the sitaution more tense, and REALLY did IMO is how the Barca players hovered instantly around the ref, especially that fuck Valdes as usual. Riled up the fans alot. They did it in every scenario, pretty retarded. Doing everything possible to get an edge. But all in all, think the ref was good, it was only two things I think he called wrong, and it was giving Di Maria a freekick (and alves yellow? dont recall) after a complete dive early on the game (started the diving show that was this game), though linesman called it more then the ref. And 2nd is Messi body check on Arbeloa (though not as brutal as Adebayors, enough to be yellow). In general ref had decisions on lock and was pretty apt. Including the red, because it was defenitely an arguable red card, even if a more lenient ref could given yellow.