My daughter is extremely sensitive about certain movies as well. However, at 2, Finding Nemo was her favorite movie. She would watch nothing else. I am sure I have seen it over 100 times. The sharks were not her favorite part though.
Sounds like in your case, you brought your daughter to a movie theatre. I heard similar stories about young children being bothered by supposedly children's movies and in a lot of cases, the movies were seen in a movie theatre.
I really can't help but think the problem could in some cases be the additional anxiety from the big screen and/or the sound system. It could even be the result of already having a bit of anxiety due to the crowd or the fact the theatre is dark. Movie theatres may be great as an adult, but a lot of children may find them particularly unpleasant.
Another issue to watch out for is a child's mood will vary from one moment to another and is sometimes not obvious. The timing of when a child sees a particular movie the first time can determine how they will react to the movie. One day they can handle a certain movie or the next they cannot.
Some children are also sometimes bothered by something that you would never expect them to be bothered by. It could be particular shapes, colors or anything. A child may be scared of the grass in the movie and not the lion standing on it for instance. I had a niece who was scared of grass. When I was young, I was scared of toy people and just made all toy people or toys with toy people in them disappear without letting on.