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.
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: 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?