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: Modern diabetes management will tell a patient immediately if their glucose levels are out of the ordinary. Results are not monitored and delivered to a county jail by an outside lab. If a diabetic is sick enough, they would have obvious physical indications. The entire escape plan hinges upon these fallacies.
Plot hole: When Sally crushes a creature in the library with the bookcases, Not only is the crushed body still there, but also its arm on the floor, yet her father still doesn't believe her.
Plot hole: Ryan Reynold's character is told by the military that his phone number is being suppressed. Later on, however, the HR guy from his company has no troubles to call him back.
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: Gideon speaks to Jill about her fingerprints being all over the bear trap. When he does he says that there is a new game going on, referring to Bobby's game. However, the police are unaware of this game at this point. He can't be referring to the garage trap as he says that the game is going on, and the garage trap has already happened. (00:35:00)
Plot hole: When Dylan enters the vampire Vargas's bedroom to interrogate him, Dylan frequently steps away from the door to let sunlight in to burn Vargas, so that Vargas will cooperate with the interrogation. Vargas is in his bed and could easily cover himself with his sheets to block the sunlight, but never does.
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?
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?