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.
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.