Jake Gyllenhaal had an ear bud in during the train sequences, into which the director would start playing music at any point in time to help Gyllenhaal's character look disoriented . The director played random songs as well as "static buzz" at times.
The only thing in the back of the white van that is real is the stars and stripes box. The rest was made by visual effects (or VFX).
Because he effectively doesn't share any scenes with Vera Farmiga and Jeffrey Wright, Jake Gyllenhaal deliberately stayed on after filming his scenes to provide voicework that his two fellow actors could bounce off.
Beleaguered Castle, a military project code name for the unit that runs the Source Code project, takes its name from a variation on the game of solitaire.
Scott Bakula: voice of Colter's father. Bakula starts off his phone conversation by saying "Oh Boy". That was his trademark line from Zurück in die Vergangenheit (1989), which has a similar plot to this film.
Duncan Jones: [Chesney Hawkes] Christina's ringtone is The One and Only by Chesney Hawkes, the same song that Sam's alarm plays in Moon (2009).