Trivia: When John and Jane are questioning their former apparent target near the end of the film, look carefully at the guy's shirt - it's the logo from another Brad Pitt film, Fight Club.
Trivia: Nicole Kidman was supposed to star along side Brad Pitt, but had to pull out due to other commitments. When she did this, Brad also pulled out but later re-joined when Angelina Jolie was cast.
Trivia: The final fight where the Smiths burst out of the shed to fight the remaining bad guys is an obvious homage to the end of the film "Butch Cassidy and the Sundance Kid".
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.