Plot hole: In the scene where Lewis and Clark nearly hit the Event Horizon, One of the crew is calling out the closing distance and another confirms this information. Regardless of clouds obscuring their view they were aware of their proximity and the fact that they were speeding towards it and forced to attempt an abrupt stop makes no sense.
Continuity mistake: Throughout the entire movie the size of the Event Horizon's interior versus that of its exterior is repeatedly off. Evidence of this is seen mostly with scenes that take place in the main access corridor. First off, it is made to seem that the ship has one central connecting tube, but in the exterior shots there are several tubes that make up the middle of the ship. This is pointed out when Miller is making his way across the ship to get to the air lock that Justin is about to open. Second, the length of the tube (heck even the whole ship) is too small in relation to how the ship appears from the outside. This is pointed out in a few different places in the movie - when the crew is up on bridge, then race all the way to the airlock in the middle of the main access corridor, where Justin has just closed the inner door and when the doctor is asked to go grab his med kit from medical, which is across the ship and he is gone only a few seconds, and also when Miller is running though the corridor to activate the explosive charges. Since the ship has no faster means of transportation, such as turbolifts or a tram system, they could not be covering the distance they appear to be covering in the movie.
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.
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.
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.
Plot hole: The entire story line around the CO2 scrubber canisters is kind of ridiculous. The Event Horizon was massive, with a crew that only inhabited it a relatively short time (since they all died in short order after attempting the jump), meaning most of its CO2 canisters would still be good. It would have had large reserves of good canisters. Plus, the ships are equipped with stasis pods, meaning they wouldn't need CO2 scrubbers for 99% of the trip anyway.
Factual error: When Justin is in the air lock and activates the outer door he freaks out as he sees the veins in his arms bulge and then he starts bleeding from his eyes and maybe his mouth too. This wouldn't happen. Movies get this wrong a lot. All that would happen is that he would lose gravity, he would be sucked out of the ship and unless he was holding his breath tightly the air would rush out of his lungs. He would die within about 30 seconds from lack of oxygen, maybe 60 if he was holding his breath, but he would not bleed from anywhere.