Plot hole: Clint Eastwood's whole investigation/solution is based on him suspecting that the victims had a common tie, rather than being random. The problem is there is no reason for him to think this - there is no reason given for them to not be considered random victims. For him to think otherwise was a bit far fetched. In the book, however, they were all on the organ donor list, which led him to the fact they all had the same rare blood type and so on.
Suggested correction: Not really farfetched. It's a common plot device for a cop to look for a link. When he finds out Gloria gave blood, he remembered the sticker in the other victim's car.
Plot hole: When Austin and his father Nigel disagree as to how to proceed after Goldmember gets away, they part ways. So why does Austin take his father's car? (01:06:25)
Plot hole: When the FBI finds out that Dolarhyde knows where Graham lives, they send a chopper and some agents over to Graham's house to pick up his wife and son. His wife is startled by the noise of the chopper SUDDENLY appearing without any warning. How could she have not heard the chopper approaching or seen the light?
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: It's never explained how Ms. Pearly the landlord knew Craig and Day Day since they were kids, and it also doesn't make much sense how Craig and Day Day are so scared of Damon and can correctly recall him being this super buff grown adult, when he was locked up for 12 years and their characters are all in their early 20s.
Plot hole: When Hundert hits the ball into the window of Mr. Woodbridge's car he keeps standing there for a moment with the club in his hand while the boys run away. Woodbridge looks in his direction and should have seen him, however, he starts asking around who the culprit was. (00:44:20)
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?
Plot hole: How can they have gotten confirmation to launch the missile from Moscow if the insulation on their transmitter was damaged? If it was a separate transmitter, why not use it in some way to contact Moscow during their crisis?
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).