I've never seen the remake of The Fugitive, but I've heard people complain about the scene where Harrison Ford leaps into the water. I guess it's supposed to be a shocking scene in the film.
Personally, the one thing that really bugs me is, as I'm watching a film, I remember scenes from the trailer and know that certain characters aren't, for example, dead because they have done that part in the film, yet.
This can ruin the "Surprise! The villain isn't really dead, yet!" moment.
OTOH, I've heard some pretty funny stories about trailers.
First, there's the story about the US distributer of one of the first of those old Hercules movies. When he showed the trailer he cut to a friend (or business partner), the person said that he put all the good parts in it and that no one will want to go see the film.
The distributer remarked, "No. When the audience sees this, they'll think, 'Wow! If this is in the trailer, imagine what's in the film!'".
In an interview a few years ago, Joe Dante, director of The Howling, Gremlins, Matinee, etc., talked about how he began his career cutting trailers for Roger Corman's production company.
One day, he and the guy he was working with were having trouble with the film they were working on. The movie was so bad, they were having a difficult time trying to make an exciting trailer.
Finally, as a bit of a joke, they edited in an exploding helicopter from another film. Surprisingly, it looked like it fit in the movie, so they left it in.
Eventually, it became a running gag. They inserted that same helicopter explosion in every single trailer they cut from that day forward. And the funny thing is that it always looked like it belonged.
In another interview, Dante talked about the trailer for The Howling. I've never seen it, but it apparently never reveals that the movie was about werewolves (it's hard to imagine how that would be possible...I guess it was cut like a murder thriller). I don't know if Dante cut it or the studio did, but he complained that people who would want to see a werewolf film didn't go, and the people who saw the movie in theatres were surprised by its contents and some of them weren't happy about it.
Sort of like the one for Fight Club. Everyone I know tells me that I would love it, but the trailer so turned me off, I still haven't seen it.