Plot hole: Had one or more locomotives coupled onto the real runaway's front engine, or even just been pushed by it, anyone aboard the "rescue" engine could have just walked to the unoccupied ones and shut them down - no copters or fireballs required.
Plot hole: In the end, all they have to do is ask the President, when he's conscious (Liev didn't kill him; he just knocked him unconscious), who killed everyone in the control room and nearly killed him. He would know who the traitor is and it's not Salt - when they look back at the facts, they'll see how Salt only killed when she absolutely had to, and how she saved lives and stopped a 3rd world war.
Plot hole: When Andromeda and Perseus wake up on the beach, Andromeda tells Perseus that Argos needs a new leader/king. The problem with this is there is nothing onscreen to show that she even knew her father the King had died. She was hanging by her arms facing the Kraken and she couldn't turn around. By the time her father died, she was already falling into the sea, so again, she shouldn't even know her father has died.
Plot hole: If the cars are assigned on a "first come, first served"-bases, how can the tv programme have footage of the drivers posing with their cars, seeing as not all of them survive?
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: 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: 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: 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?
Suggested correction: Not necessarily. Some engines may not have a rear cab access (like Frank/Will's engine had). And even if the rescue engine did have a rear cab access 777's engine only had a side access stair which at the speed it was going is more difficult to climb over from the engine in front of it.
Actually 777's catwalk goes across the front, from side stair to side stair, but someone would have to leap over a rail or a chain to get onto it from the other engine. Why would there be stairs on the right side unless there was a catwalk to get to the door on the left side?