First, the referee gave a red card to an offense that could have possibly not even been blown a foul without too much controversy. At the very worst, it was a yellow card, not the straight red that left the Florentines down a man for the final 14 minutes. The story I'm linking to calls it an obvious, deliberate elbow to the throat. To me, it was a guy who had already poked the ball away, and had lost his balance. His arms were out yes, but to say it was a deliberately aimed shot with the elbow is something that I would not being willing to say.
Then, in the closing minutes of the game, the linesman and the main official combined to miss what was obviously an offside Klose who punched home an easy header to score the game winner. It is easy to hit the game winner when you are 5 yards offside. It was the most inexplicable blown offsides call I've seen in recent memory. I've been searching said memory, and I can't recall a worse one.
I don't know what UEFA can do about it after the fact, but the only right and fair thing to do would be to strip that goal ahead of the second match to be played in Florence. I doubt that is an option, but if officials are going to blow calls like that, it absolutely should be.