Audio problem: This scene is repeated multiple times in the movie: usually when the main character enters the "source code" the scene begins by panning over a small pond showing a Canada goose taking flight. However the sound editor makes the mistake of dubbing in a recording of a hen mallard duck.
Revealing mistake: Every time Colter finds the bomb, the cell phone used as the detonator, is running a Adobe Flash movie named "HISTORY.swf" on its screen. The Adobe Flash Player logo is visible in it. When he removes it the first time and tries to call back the bomber, it's nothing but a Flash animation sequence playing on this mobile. (At about 01:11:20) Finally he finds the secondary mobile at the back of the bomb, and this too has a HISTORY.swf playing in it. (00:15:30 - 00:55:00)
Factual error: Several uniform items on USAF Captain Colleen Goodwin are incorrect. She is missing several ribbons and then ones she does have are out of order. A USAF Capt would have a Basic Military Training ribbon and (probably) at least one Good Conduct ribbon and one Longevity ribbon. It is also unlikely that she has enough time in service to be wearing the Kuwait Liberation Medal ribbons. The ribbons she is wearing are out of order. The correct order is from top left: Air Medal, Joint Service Achievement Medal (JSAM), Organizational Excellence Award, Kuwait Liberation Medal (Saudi Arabia), Kuwait Liberation Medal (Emerate of Kuwait). (In the movie, Capt Goodwin is wearing from top left: Org Excellence, Air Medal, JSAM, KLM-SA, KLM-Kuwait). The blue name tag is not worn on the USAF service coat. It should be nickel plated with a matte finish.
Continuity mistake: Multiple scenes: On every exterior shot of the train, you can only see one row of windows across the upper galley section. However, whenever there is a scene shot on the upper 'galley' level, there are two rows of windows, one right above the other. The external shots were filmed using a Chicago Metra train (which uses 'bilevel' galley cars), the internal scenes were filmed on a set in Montreal, Canada.
Continuity mistake: In the scene where the bomber shoots characters played by Jake Gyllenhaal and Michelle Monaghan, when filmed vertically, there's a splodge of blood in front of Michelle's face. However, when the camera is on the ground, filming her face, there's not even a vestige of blood on the floor when it should be exactly in front of her face.
Factual error: Dr. Rutelege calls for a detachment of MPs who arrive wearing MP brassards, but in the USAF they are known as Security Forces. (01:21:30)
Other mistake: When the conductor / ticket inspector is checking tickets, why doesn't he check Christina's?
Continuity mistake: When Colter fights the guy in the brown coat at the train station, the sun changes between shots.
Other mistake: When the bomb explodes the whole train is consumed by flames. The device is apparently located in one carriage and any explosion would be localized to an extent and would likely derail that part of the train, but the whole train explodes as if it was pumped full of gas.