Don't think that was Ramois doing the pulling, think that was Busquets. I'd have to say that was a good shout for a pen, and should have been if the ref saw it. The other supposed "pen" from a foul by Ramos sliding in.. don't think that was a pen, strong challenge.. it's what usually gets Ramos sent off... but he did make contact with the ball.
Croatia had a couple of good chances though, Rakitic had to take that one from Modric's cross.. you really won't get many better chances against Spain due to the amount of time you spend chasing.
He first had a contact with the player and then with the ball if I recall correctly... I think that counts as a foul and penalty/16 meter line free kick and yellow/maybe red card...