Plot hole: So humanity in the future managed to solve time-travel, but is unable to develop armor-piercing, exploding ammunition? And it uses old, untrained civilians as soldiers to fire M16-16 and WW2 heavy machine gun ammunition at fast moving targets, instead of developing rapid-fire computer-targeted guns? The movie shows 0.5" ammunition (from said WW2-era machine gun) CAN take out the Aliens, so? (Not to mention flame-throwers, shown as effective but sparsely used, no tanks, etc).
Suggested correction: The rifles the civilians are equipped with aren't M-16s; they are modified BCM carbines "MK III" and "MK IV" with HERA Arms CQR furniture.
Plot hole: When the survivors first make an attempt to break out towards the station they kill numerous assailants at close quarters and yet only one of them (Uno) is infected. There must be dozens of the parasites floating around, enough to infect them all.
Plot hole: If the gasoline in fuel lines and tanks is reaching flash point and exploding, there should not be so many cars just sitting around. Surely all of those vehicles' tanks are not dry.
Plot hole: There is supposed to be no power when the Dragonfly ship reaches the island, but the lights are still on. At first, I thought it was just a lighting trick, but you can see the lights are on in the tunnels.
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.
Suggested correction: It can be assumed that the jettisoned module has enough "jettison power" to force it away from the command pod. And in turn that force would move the pod further towards the Tet. It's reasonable to assume the Tet couldn't pull the module that was moving away, under dramatic force, and to which it didn't have line of sight (which was blocked by the pod).
Plot hole: Although Marty rips the fuel line, not all the fuel would have drained out of the tank. Only the fuel that was already in the fuel line would have leaked out, meaning it could simply be patched, bled and the engine would run without a problem.
Suggested correction: A cut fuel line could absolutely drain the tank. Even if not a direct route with respect to gravity, it could still create a siphon effect and drain the tank.
Plot hole: When Delila finds out who Jimmy really is, she takes his tuxedo and is apprehended by the bad guys. She then turns on her homing device on her necklace. The office says it will take 20 minutes to get to her. From that statement to when the CSA finally arrives, Jimmy has time to go to Devlin's, write him a letter, discover water striders, find his suit, and get back to Delila and fight the bad guys. THEN CSA shows up. The timing is really off.
Plot hole: After Nanahara and Noriko run away from Akamatsu at the school, Niida shows up from behind some bushes opposite the school and inadvertently kills Akamatsu with his crossbow. But Niida is Boy 16, which means he should still be in the school building (he's supposed to come out after Noriko, who's Girl 15). There's no way he has any time to get into those bushes.
Plot hole: When Daniel is in the air with the stolen plane from the Los Alamos air base Nat suddenly appears from behind. However, Nat had no chance to slip into the plane secretely as there was only one stepladder that had been in his mom's full view while she hugged Daniel good-bye. (01:25:30)
Plot hole: We discover that Teresa the maid has been turned into some kind of living zombie at the end of the movie. She confronts Alex and Megan near the end, and they run away from her and then fight with the Puppet Master. The issue of Teresa is then never addressed in the rest of the film, she just simply disappears from the plot and the scene. (01:13:35)
Plot hole: If the dinosaurs are so dangerous, why are they only kept behind plastic sheeting at the back of the truck, rather than in cages? There are computers in the truck, so obviously people must go in there, and it wouldn't be very safe to use computers if dinosaurs were roaming free in the trucks.
Plot hole: During the end of the film chase scene, Agent Mackelway calls Agent Kulok and gives her a vague location of where they are and asks for back up. Considering Mackelway had been kidnapped and driven out into the country, it should have taken Kulok much longer to arrive at the scene instead of the few minutes that are indicated.
Plot hole: While still unsure where and when they are, the Nimitz has two F-14 Tomcats aloft, investigating a pair of low-altitude radar contacts. They determine the planes are WWII-vintage Japanese Zeros in full military livery. The Tomcats are told to shadow the Zeros without engaging them. Then, the Captain, the XO, the CAG and Lasky all go to a formal dining room and sit down to tea. In this scene, they talk about many other 1941-era things that are happening, but nobody mentions the Zeros. That fact, and that they left their Tomcats where they did, suggests this scene was meant to be in an earlier part of the film (when things seemed odd, but no imminent threat existed) and got moved here, creating a plot hole that the USS Nimitz could slide through sideways. US Navy nuclear carrier command staff wouldn't simply go have tea under the current conditions. (00:40:30)
Plot hole: How did Carolyn Fry get out of the cave in the canyon to confront Riddick at the Skiff? Riddick strained to roll the rock into the cave entrance, and he was a big, strong man from a position of good leverage. How did Carolyn and the other two push the rock out of the way so that Carolyn could get out? And, then, how did Carolyn mange to push the rock back into place? It was still there when she and Riddick came back from the Skiff to bring back the other two.
Plot hole: After Riker takes the Enterprise through the Briar Patch to communicate with Starfleet he returns to rescue Picard from the collector in mere minutes, even though it was supposed to be a 2-day journey.
Plot hole: When the umbrella ops first get onto the train, rain has to power it up. There were plugs disconnected, and you see a hole in the fence as she shines a flashlight on it. It can't be anything infected because they didn't power down the red queen yet, and release the bioweapons. The red queen isn't physical, just controls systems. And with none of the zombies, or other infected loose yet, what else could have unplugged it? Spence was knocked out on the train, this seems to be a plot hole. (00:02:00 - 00:20:10)
Plot hole: When Peyton/Darkman is showing Bridget how the liquid skin works, he drips a small amount onto his burnt finger, and it solidifies. However, when he drops it onto his finger, it magically shapes itself into a replica of a perfect, undamaged finger. This makes no sense, as it is simply a liquid and is not being molded by any forces. Hence, it should not look like a perfect finger.
Plot hole: When the asteroid first approaches Earth it does so very quickly, but then it takes hours to finally enter the atmosphere and land on Susan.