Deleted Scene: Quite a few actually, and all will be on the home video release, including Colin's suicide. Also the final scene where Lars is chasing down the thing-wolf was omitted in at least one DVD version.
Executive Meddling: A lot of the film's runtime was cut in favor of the action scenes. The animatronics for the film were also ditched for CGI. In fact, many of the CGI shots were simply "painted" onto the already filmed animatronics simply because someone higher up thought that look would be better for the film.
The special effects crew were fairly annoyed that their hard work was masked or replaced with CGI. They later started a Kickstarter campaign to fund Harbinger Down, a movie designed to show what could be accomplished with entirely practical effects.