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 Claire is getting interviewed at the FBI building, there's pics of inside the bank during the robbery, even though the security tapes were destroyed in the microwave.
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: 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 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?