Every player have bad games and Pedro is not excluded. Overall he been playing great the whole season, and I'm fine with him having one bad match.
The fact is that Tito always uses either Pedro+Messi or Villa+Messi but never all of them at the same time. Playing with 2 great forwarders is not enough (because technically the third, such as Tello or Alexis, don't really have much presence in the game, and defenses don't seem to care about them). I know that if we get our MVP trio again it will for some make things easier for Villa & Pedro to shine, because both of them will help each other to have more free spaces, and that includes Messi.
I'm not gonna write what I've said before. There's a fix for that and Tito did it last game. When that happens, play Villa as a 9 and problem fixed. However, Messi should go to the right wing when that happens and it would work even better. Imagine 4 defenders annoying Messi from the right: Villa will score easily. And if it's the opposite, Messi will score easily as well. Win win.