The Lewis and Clarke crew enters stasis on the way to Neptune, made necessary because of the "30 Gs of acceleration" they will endure for the trip. When they arrive at Neptune, however, there are coffee cups and other debris on the tabletop, loose chairs, etc., in the same position as they were before the trip. This is not consistent with sudden and severe acceleration.
Upon first entering the Event Horizon, Captain Miller comments on how the ship is a "deep freeze" and how there are ice crystals everywhere. Immediately after this, we see a water bottle floating around with liquid sloshing inside it.
Just after helping Weir to his feet and as he turns away, you can see that D.J's shorts are completely dry on his backside, despite being in a tank of liquid for the last 56 days and being visibly dripping wet from the front.
Just before Miller jumps through the closing door escape the fire in the 'meat-grinder', there are several very short cuts from various angles. During the very last cut which shows the fire coming head-on towards the camera, the meat-grinder is not revolving. Throughout the entire film, apart from that moment, the grinder is consistently turning.
When Justin is ejected into outer space, his veins immediately start to burst and bleed heavily. This isn't very likely to happen in the short time that he is exposed to the vacuum of space. Parts of the body will probably start to bulge due to the lack of atmospheric pressure, and there will probably be some subcutaneous bleeding from ruptured blood vessels, but the human skin is thought to be resilient enough to stay intact. Also, the blood that leaves his body remains liquid; in reality, it would boil and evaporate instantly due to the lack of pressure. Not everything about the scene is unrealistic: the fact that he remained conscious is probably correct (most adults would remain conscious for 10-20 seconds), as well as the fact that he does not freeze (although deep space is extremely cold, the lack of gas molecules makes it difficult for body heat to leave the body).
"Liberate tutemet" is wrong in Latin. "Liberate" is 2nd person PLURAL imperative, "tutemet" is an emphatic 2nd person SINGULAR pronoun. The correct version would have been "liberate vos" or "liberate vosmet". "Tutemet" (which is a very rare form) is also wrongly nominative: an accusative is needed in the sentence for the object of the verb "liberate".
When Dr. Weir plays the record of the emergency signal containing the "Liberate me" bit, D.J. says that he can't make out the rest of the message, but Dr. Weir always stops the tape immediately after Liberate Me has been spoken, so D.J. wouldn't have been able to hear any other part of the message to begin with.
Miller's rank is "captain", as shown by the four-stripe insignia on the shoulders of his jumpsuit. Yet his leather jacket shows two silver bars on the shoulders, which is the insignia for "captain" in land and air services, a much lower rank. As the service shown in the film is modeled on the U.S. Coast Guard, Miller's jacket should show a captain's silver eagle.
As has already been mentioned in one of the other goofs, there is no atmosphere in space and even thought the temperature was at absolute zero, body heat would not be rapidly lost: no atmosphere means there's nothing to conduct the heat away nor to radiate heat away. The drifting crew members would not turn into space popsicles and limbs would not shatter a la Terminator 2.
As the Lewis and Clarke approaches the Event Horizon somewhere near Neptune, it goes trough multiple cloud formations. However, all later scenes happen in zero gravity making the presence of any atmosphere impossible at that particular level.
Although the ship is referred to as a 'deep freeze,' twice we see a bottle of sloshing water floating about the Event Horizon, at the very beginning of the movie, and just before the rescue crew boards.
There is no gravity on the Event Horizon. The movie makes a point of showing magnetic boots keeping everyone on the floor. Yet when Justin is sucked into the "heart of the ship", the resulting shock wave hits Capt Miller and he is thrown against a wall. He then falls to the floor, instead of floating in the air like the rest of the loose debris on the ship.
At 55min Starck says that CO2 levels will become toxic in 4hours from that moment. Furthermore, they brought CO2 scrubbers back to the Lewis&Clark and then that ship exploded. So how did the rest of the crew survive in a toxic environment and without the scrubbers?
Near the end, when Cooper watches the "blood" flowing above the ceiling lights, the front of the flow does not change shape at all and also, just before the camera changes, briefly jumps backwards, revealing it to be a plastic printed film above the light fixtures which the light is merely shining through.
When a fully possessed Weir grabs Miller's forehead and squeezes, blood seeps from Weir's fingers down Miller's face and scratches are seen after he lets go. But Weir's fingernails clearly never dig into his face at all, so there should be no blood or scratches.