I don't have a problem with a child or adult calling a clownfish "nemo" or hippo tang "dory", but it dpes annoys me when I am in the LFS and there are 5 children banging on the glass of the "nemo" or "dory" tank (no matter how many signs are posted). That all comes to the parents' disciplining their child though, not the movie promoting a few fish.
It also bothers me that everyone tries to get "nemo" and "dory" together in their small 10-20 gallon tank. That irks me because they never want to hear that these tiny hippo tangs need huge tanks. Again though, that is not really the movie's fault, it is the people's ignorance and selfishness.
I think the worst thing the movie did was the tank in the dentist office. Since that movie, I have seen a lot of people try to replicate that tank. Maybe if the movie would have put appropriate species into the tank, it would have been okay, but they did not do that. In that tank was a cleaner shrimp, porcupine puffer, butterfly fish, starfish, and moorish idol. There are so many people who try to replicate that tank that I think that is the worst part of that movie. Even on this message board, the topic comes up every 2 to 3 months with someone saying they want to try to replicate this tank in thier 55 gallon aquarium. That is the only part that I have a problem with.