Plot hole: Anderton's wife gains entry into the jailhouse using her husband's eyeball - but he's already locked up inside, so his eye would not still have access to enter as it pleased. Any place anywhere that would have any sort of security system requiring anything from a simple passcode to a card key to a retinal scan, would immediately delete the user in such instances from all rights. And would also certainly report on any attempted use of such (retinal scan, pass code, whatever). (02:00:45)
Plot hole: When Amidala and some of the clone troopers get blown out of the ship chasing Dooku, later the trooper approaches Amidala and asks about making their way back to the front lines, but Amidala says they should go to the hangar to help Obi-Wan and Anakin. How did she know about the hangar, having left the ship quite some time before it arrived at the final destination? (02:05:50)
Plot hole: The Americans allegedly landed at Manchester on their way to kill the male Dragon in London. London is due south of Manchester. Why then did they head in the complete opposite direction to Northumberland?
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: 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: 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: During the nova scene, everyone is tying down the sails after securing themselves with lifelines to the mast. Jim and Silver are on the front and Silver is knocked off. Jim is then all dramatic and runs to grab Silver's lifeline which seems to be coming from above, and pulls Silver up like a pulley. How come? The lifelines were attached to the mast, so Jim's action is pointless... even if he could do it, because a shot later both lifelines are streaming right to the mast, leaving no room for a pulley of any sort.
Plot hole: In the scene where Richard Gere is looking at his reflection in the motel bathroom mirror, he imagines smashing his face into the mirror. When the phone rings, breaking his hallucination, he still has blood on his hands but it is never addressed.
Plot hole: Although the errand bird always insists on the postage and even asks for additional fees for more than twenty words, he never gets any payment from the assigning characters.
Plot hole: When Alexander is traveling into the future and goes through the ice age he is visibly affected by the extreme cold temperature outside the time bubble. However when he stops in the future when the moon had been destroyed then continues he is not affected by the explosions and extreme heat around him. Based on the effect the extreme cold had on him (frost on his face and hair) he should have been roasted alive.
Plot hole: Throughout the movie, the flies are vulnerable to light (direct sunlight and even lightbulbs) to the point of incinerating in a split second. Except... they are not; in several sequences they fly to and from bodies and without even taking a direct path (look at all the action happening in front of the house, by the cars, in broad daylight).
Plot hole: When someone is in a coma for 28 days, the hospital would have AT LEAST have catheterized said person, however when Jim wakes up in the hospital he is not attached to anything but an IV.
Suggested correction: What happened when Jim was admitted is never revealed. Being that there is nothing to show what happened when he was admitted its impossible to say certain procedures would have been followed or more simply the hospital might have not undertaken them. More importantly we don't know when the virus hit certain areas. In addition Jim was taken in around the time the virus was first starting to spread and hospitals would be the most likely place someone infected would be taken to so many working or staying there would have been the first to have been infected. With that scenario the staff at the hospital might have neglected some of their patients because of how quickly the virus spread.
If the hospitals would have been some of the first infection sites, why would Jim have survived the entire 28 days? I doubt someone was refilling his IV on a regular schedule if the patients are becoming violent animals, which would suggest he would have died of dehydration before starvation would have gotten to him. Also, why would those infected ignore Jim while he was comatose? Would it not be 'sporting'? Given how instinctual they seem to become I don't see how comatose would be any different from intoxicated or deeply asleep. Did all of those sorts avoid infection as well?
Suggested correction: I thought that this was a mistake as soon as I saw it on screen, but reconsidered. It's perfectly possible that there was some, probably human caused, delay in updating the security system. After all, there wasn't a rush to do it since they already had the chief on ice. Maybe the sleep jail was still on a legacy system without automatic updating. Just assuming that in the near future that all systems are all perfectly integrated and instantaneous does not validate this as a mistake.