Revealing mistake: In the scene where Sam Neill has set the bomb to blow up the rescue ship, Laurence Fishburne comes running up to the sealed door of the Event Horizon whereupon it shakes back and forth like a stage door would.
Revealing mistake: During the opening scene, when the camera is starting to zoom in on the ship outside earth's atmosphere - the view of the crew inside zooms in quicker than the camera moving in to zoom into the cockpit.
Chosen answer: The movie never explicitly says; but science is as yet unsure what happens to a given piece of matter once it crosses a black hole's event horizon, so who knows? The ship could have been thrown seven years forward in time, or far enough away that it took seven years for it to drift close to Neptune. Pick any explanation you like.