Plot hole: According to the flight recording, Odyssey was on an uncontrolled pull towards the Tet as Jack says, "We're not getting away from this thing." So even if Jack jettisoned the sleep module where Julia was in, the module should not be able to get away as the whole ship is being pulled towards the Tet.
Plot hole: When the HAB breached, killing all the live plants and bacteria in the soil they could have been replaced. He had plenty of potatoes to use as starters, and he had his human waste from the time of the first planting to replace the biomatter and bacteria. It may have been a smaller "garden" but he still would have been able to replant. (01:07:00)
Plot hole: At the end the police shoot Cole while he was chasing Dr Peters but the police do not stop Dr Peters and question him as to why a man was chasing him at the airport with a gun, instead he is unchallenged and allowed to continue his journey.
Plot hole: During the warp-speed chase, the Vengeance literally blasts the Enterprise to pieces, and dozens if not scores of Enterprise crew members are killed and injured in the carnage. The medical crew, including Chief Medical Officer McCoy, should have been working feverishly on the wounded and dying for hours, at least. Instead, as Kirk asks Khan for help, the Sickbay is practically deserted, and McCoy is almost idly conducting blood experiments on a dead tribble. There's no sense of a catastrophic medical emergency whatsoever. It's as though the Sickbay sequence was shot for a different script in which there was no emergency, and then lazily inserted into a rewritten script.
Plot hole: When the old women are painting the eggs, you can see them blowing the yolk out of some. Why didn't they blow the yolk out of the Critter eggs?
Plot hole: WW mentions that "As Darkseid waged war on Earth, he found a secret there", that being the Anti-life equation. But later on it turns out that after being defeated, planet Earth is so "anonymous among a trillion worlds" that he never manages to find it again and destroys another 100,000 worlds (his words!) to look for it again. That would mean that they lack any sort of navigation, and it's hardly possible anyway that the planet would be "anonymous" when it contains what Darkseid wants the most.
Plot hole: After E.D.I. goes rouge, Kara brings up his weapons list, which consists of 2 ThroatRippers, 2 ShockHammers, and 3 Blue Ferrets, so E.D.I. has 7 missiles. He fires two during the Russian dogfight, another two when he and Ben escape from Alaska, and another two at the Korean border - one of which is the last missile. That's 6. So where did the last missile go?
Plot hole: Summer vacation couldn't be taken away just because it is winter, (or just snowy), they could just go by the date.
Plot hole: When Abby and her kids are abducted, the sheriff is sitting right outside her house and sees this happening. Yet the video didn't record. Well the sheriff saw it all with his own eyes so why wouldn't his testimony hold up? The tape actually shows the UFO so there's proof right there. (01:08:55)
Plot hole: After Dr. Ashford was shot, he stayed down the whole time that Alice fought with Nemesis, they fought with Umbrella, and after they took off. How is that possible? According to all the other times they've been shot, and with the t-virus in their bloodstream, they reanimate almost ten minutes later -- not when the director wants.
Plot hole: While a tracker can certainly make it so that Junior knows where Brogan is at a given moment, it is impossible for Junior to know where exactly the plane is going to land and be lying in wait, with Brogan walking right past him. Junior would have to be well ahead of the plane in order to do that, and know exactly what direction Brogan would walk to cut him off and ambush him.
Plot hole: If Marybeth was able to seal her nostrils and use her extended finger to remove the cap and make nobody suspicious about her, why didn't Delilah do the same thing? She was alien, so she should've still been able to do it, same as Marybeth.
Plot hole: If the cars are assigned on a "first come, first served"-bases, how can the tv programme have footage of the drivers posing with their cars, seeing as not all of them survive?
Plot hole: When Gwildor tells Julie and Kevin that he can use the Cosmic Key to take them to any point in time they wish, Kevin asks just for them to go straight home. As Kevin and Julie go through the portal, Julie turns around and shouts to Gwildor to send them back before being dragged through the portal completely. When Julie wakes up in bed, she discovers that Gwildor has sent her back to the day her parents were killed. Julie never said where in time she wanted to go, so there's no way Gwildor could know to send her back to the day her parents died.
Plot hole: When the aliens kidnap the adults, the kids are left behind. But all the kids seen are around 11 and younger. Where are the teenagers or young adults? None of them are during the celebration scene nor in the arena on the alien planet.
Plot hole: Hock sneaks a gun into the prisoner interrogation area because he is told that guns are not allowed there. If the prison was so strict about keeping guns out of that area then they would surely have metal detectors to prevent such a thing from happening. (00:15:25)