The movie fictionalized much of Eric M. O'Neill's story. Among the changes made for the film: The real O'Neill knew going in that Robert Hanssen was the subject of a counterintelligence investigation. There was no cover story about sexual perversions, and no dramatic meeting where O'Neill learned the truth. There was no extensive contact outside the office between O'Neill and Hanssen as shown in the film (e.g. O'Neills visiting the Hanssens, Hanssens dropping by O'Neill's apartment); however, Hanssen did take O'Neill to church. The scene where Hanssen takes O'Neill out into the woods and drunkenly fires his pistol is fictional. Unlike in the movie, O'Neill never saw Hanssen after the arrest. While O'Neill did obtain Hanssen's PDA, he took it to FBI techs to download rather than downloading it himself.
When Hanssen's car is thoroughly inspected his trunk contains several assault rifles including German Heckler & Koch G36s. The film takes place early in 2001. HK did not announce the release of the G36 until Spring 2001 and did not begin releasing free LEO (Law Enforcement Only) samples until 2002. It is also unlikely that Hanssen would even be issued such as gun as he did not test new firearms for the FBI.
Eric and Robert enter a church and Eric makes the sign of the cross incorrectly. Since much of the plot involves Eric's and Robert's Catholicism, it would have been an error that would have made Robert suspicious.
When Eric O'Neill removes Robert Hanssen's Palm Pilot from his briefcase you can clearly see the Palm Pilot Model is a Palm III, which doesn't use an SD memory chip, which is lying next to it. This Palm has a 8 meg of internal memory only - no External memory card.