The Goonies
The scariest part of The Goonies was easily the scene with the octopus. Although "the octopus" was mentioned in the film's theatrical release, that scene was cut from the original version. It was later added back in for the rerelease on Disney Channel.
Jurassic Park
If you're a fan of this Spielberg classic, you might recall the scene in which giant velociraptors chase Lex and Tim Murphy through the kitchen, but unless you were looking very closely, you might have missed this: When the first dinosaur enters the kitchen, you can faintly make out one of the crew member's hands guiding it into the room. Whoops.