Continuity mistake: When John and Jane reach home after racing each other from the restaurant and she crashes her car into his, he's wearing a black jacket just before she hits him and no jacket just after. (01:05:15)
Continuity mistake: Near the end, when the Smiths are hiding in the shed, from the inside the front of the shed and the door have several bullet holes (as do the sides), but in the long shot of the shed, the front is in perfect condition. (01:45:00)
Continuity mistake: When the Smiths steal the van from the Coleman's, a cross on a rope is hanging from the rear view mirror. During the BMW chase, the rope goes from being almost a foot long to about two inches long. (01:23:30 - 01:24:40)
Continuity mistake: While being chased by the 3 BMWs, the passenger's headrest of the Dodge minivan driven by Brad changes from a 1-piece (part of the seat), to a headrest that you can adjust the height and it keeps changing during the scene.
Continuity mistake: When John sees the BMW's in the rear view mirror for the first time, the cross hanging from it disappears. (01:24:30)
Continuity mistake: The second time John and Jane enter the elevator, they both have machine guns. However, when they exit, Jane is holding a handheld pistol and they have swapped sides. (01:42:00)
Continuity mistake: When Pitt is chasing after Jolie, he crashes through a fence and fires his gun, hitting the car's windshield. To the left of where Pitt is, you'll notice that there's one rail missing in the middle. When he climbs through the fence to the street, the fence rail has returned, and the hole left by Pitt is now slightly wider, just enough for him to climb through. (00:45:40)
Answer: It comes down to a deleted scene. And I remember it as clear as day from when I saw it at the cinemas. There is a scene where Jane is brushing her teeth at the basin. John walks into the large bathroom and begins to take a leak. As John finishes up, Jane looks over her shoulder at him, just in time to see him lift one leg and give it a couple of sharp shakes. Later in the movie, after the ailed assignment/shootout in the desert, Jane is watching the footage of the other assassin doing the very same memorable action. Right as she is in the middle of replaying it back a couple of times, John turns up at her building, and one of her agents who has answered the intercom says, "Jane, it's your husband." And that is when the penny drops! For some bizarre, unknown reason, they removed that very important key bathroom scene from every TV and DVD release, leaving people who did not see the theatrical release at the box office asking the question of how Jane realized it was her husband.