Factual error: When D.J. is attacked by Dr. Weir, he is grabbed by the throat and is squeezed until his windpipe is broken, shown by the way he was breathing (or struggling to). When Weir seizes him again and throws him against a support beam, he screams in a way impossible for someone who just had his windpipe crushed.
Suggested correction: Dr. Weir doesn't crush DJ's throat at all. The noises he makes are simply choking noises because he is being picked up by his throat, there isn't even anything in the scene to imply his throat is being crushed, which in reality requires considerably more effort than most people believe.
Continuity mistake: In the last few scenes where Lt. Starck is getting ready to prep the Gravity Pouches, the tube in front of her fills with a bloody substance, then shatters, sweeping her away. She then falls down a hole in the floor where the ladder is. Later, when the tube is whole and the blood gone (showing that it was a last ditch scare attempt from the ship) she still has blood on her face. It couldn't be from the fall, either, because she landed on her back and wouldn't be bleeding from her hair line.
Suggested correction: The blood was real. That's why you see it on her face. It wasn't an illusion and the blood isn't gone, it just drained away through the grating.
Plot hole: The use of massive explosives to separate a ship makes no sense as the explosion would send fragments at high velocity in every direction guaranteeing it would penetrate whatever ship is remaining. As we see in the final scene when the ship does blow apart, it is not a precise controlled detonation to sever connections but a total (and glamorous) explosion which makes no sense whatsoever.
Suggested correction: The explosions breach the outer hull, pulling the debris outward with the explosive decompression, the film shows the ring shaped explosions at both ends of the corridor. The debris wouldn't hit the lifeboat because it is heading in a different direction.
Plot hole: An engineer on a rescue ship seems to be the first person instead of the entire planetary intelligence community and the NSA (as reported by Dr. Wier) to translate basic Latin from what the Event Horizon's captain said. Somehow nobody else with all the vast resources of the NSA and other government organizations could clean up the transmission to determine exactly what was said?
Suggested correction: The recording of the Event Horizon's captain was taken directly from the ship's log. It was only available to the crew of the rescue ship at that time.