Plot hole: Near the end of the film, Carrie gets a quarter pipe. The problem is that there is no pavement anywhere near the farm which was expressed explicitly earlier in the film. Because of this, she won't be able to use the quarter pipe anyway, especially since it is about 2 ft at the base so they would definitely need to build the rest of the ramp. (01:14:00)
Plot hole: The water-borne biological weapon makes every individual a crazy murderer, right? Near the beginning a man burns his house with his wife and child inside. So then why do the three hunters not try to kill each other or the crazy wife in the nursery not try to kill her son?
Plot hole: Milo and Nicole go to the club and ask for John. After failing to convince the woman that he works in the senate for Kansas, the woman looks at him and calls him 'Senator' but calls Nicole 'Mrs Boyd'. There was no mention any of their names (even though Milo's surname is Boyd). If the woman calls Nicole Mrs Boyd, she surely must know Milo and that Nicole was his wife.
Suggested correction: The scene starts with the membership director telling them the club is closed for a private event, so we don't see them enter and what they say to her. They obviously cut straight to this part to cut out time. But Milo and Nicole would have given her their names so she could check to see if they're members or on the list.
Plot hole: In one of the last scenes when the scribe is putting the newly published bible on the shelf you can see next to it a big green book with the word Tanach written on it. That is actually a translated bible with the Hebrew and English, including the five books of Moses and psalms plus much more. He had the Bible the whole time. (01:47:50)
Suggested correction: From the internet movie database... The Hebrew Bible, or The Bible or "the Chumash" in Hebrew, is already in the library. The Christian "Old Testament" is the Chumash with some variations (reorder of books and reorder of the 10 commandments, depending on religious denomination). The New King James Version is an Old Testament with the Christian Gospels added at the end, some of which the main character, Eli, quotes. These two books would be considered separate and unique in a library.
Plot hole: When Moses comes to Sarah, a wet team arrives. Then, when Sarah gets free in the hotel and makes a 911 call, Cooper is on the plane and talks on the phone with someone about cheques and gets a notification about the 911 call. He comments why no one thought about that and asks the pilot to turn around. So who sent the wet team earlier?