There are a few that I don't like.
1. The catapult component of the Catapult. I, too, think the tiles are good.
2. The Count. You pretty much always need to check with everyone when someone is about to score. In a 3-player game, an hour-long game is now 4 hours.
3. Bridges, Castles & Bazaars. Echoing from above, Castles are so easy to forget and Bazaars interrupt the flow so counter-intuitively.
4. The half-sized and double-sized tiles. Caused so much trouble interpreting interactions with other expansion.
5. Messengers are not that bad, but whenever your score, you'll want to see which score-marking meeple on the scoreboard can give you a message.
6. Ferries. Just not enough incentive to put more effort on the not-so-interesting roads, especially when compared to the Inns.
7. Japanese Temples. If a modern convention centre does not blend in, how could buildings on the other side of the world?
Having finished the list, I realize that these are the bad expansions, in my opinion, from the worst to the least bad. I like all the other expansion that I have.