First impulse for an explanation would be conditioning. But I'm sure there is more to it.
Now check this out: St. Louis Cardinals - Chicago Cubs: 5:1. Baltimore Orioles - Toronto Blue Jays: 6:4. Bayer Leverkusen - Hertha BSC Berlin: 3:3. The latter is the best score they've had in about a hundred games. I'm so glad that sports isn't very important to me, because otherwise I'd be depressed for only supporting teams that suck.
They did, but they are still firm favourites to go through in my opinion. With the same dominance at home, they will be unlucky not to win by two (which they could have done today, if you look at the number of chances they created).