Other mistake: In the hunt out in the wilderness - where Jane looks in the binoculars - there is a cover on one lens - but it shows you can see both sides. (00:30:27)
Other mistake: In the scene where Jane and John race home, we see Jane smashing her Mercedes C320 wagon into John's Lincoln town car. Both these vehicles have airbags, yet they do not deploy upon the impact between the two cars. (01:07:25)
Other mistake: After the Smith's house blows up both John and Jane's white shirt's are really really dirty but when they're driving in the stolen van their shirts are bleach white again except for the blood stains.
Other mistake: When Jane is driving with John on the roof, she jumps out when John breaks through the window. The car then proceeds to accelerate through the trees and into the air. The road is not downhill and Jane didn't place anything on the gas pedal.
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.