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: 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: 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.