Plot hole: When the first security guard, who stayed back to get something to eat, hears something in the laundry room, he walks over to the washing machine where he finds the head of the other security guard inside. He turns around screaming and trips over the security guard's body on the ground with no head. Wouldn't he notice the dead body on the ground when he first entered the room?
Plot hole: At the end, there is an explosion large enough to destroy and sink an entire ocean liner, but Julianna Margulies, who was sitting right next to where the explosion went off, not only lives, but is virtually unscathed? Yeah, right. (01:19:00 - 01:20:35)
Plot hole: The dead young girl who wears white has hemophilia (uncontrollable bleeding), and her mother states that she's scared of all sharp metal objects (scissors, etc.), yet she goes to play in an old abandoned steel mill all the time.
Plot hole: The psycho coed murders her lecherous professor (played by William Shatner) by pushing him out a window. In the very next scene, she's driving around with his body propped up in the passenger seat of her car. She weighed no more than 100 lbs., tops, and Shatner was easily at least 250 when this film was made. No way she could have dragged him to her car and lifted his dead weight into the seat, no matter how much adrenalin she was pumped with. Physically impossible.
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: Mun has an eye transplant, and this gives her the ability to see the dead. However, how come she can also hear the ghosts as well?
Plot hole: Holmes asks what had frightened Sir Charles enough to make him run away from the house. But when Dr. Mortimer described the scene, he only mentioned that at one point the prints did not show heel imprints. It is an easy deduction that sir Charles had been running, but the doctor did not say anything about the direction of the footprints.
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: Towards the end of the film when Private Shakespeare is talking to the wounded soldier, his coat and hair are suddenly dry, strange when the majority of the film is set outdoors in the rain.
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?