I would add that Bayern should have had two penalties for blatant handling so it could have been 6-0. It was nice to see Barca once again out played. Real has done it often this year and the tactical genius Moureen seems to have designed the blue print.
I agree Bayern deserved the win, but the second goal was offside and the third was a clear foul against right before the goal. The 2 handballs you mentioned, one debatable and the other was more accidental. For me, the refereeing in this game was really sub-standard.
Barcelona is made to look rather one-dimensional against teams like this: physical, defending as a team, quick counter-attack and good with set pieces.