The commuter train map posted inside the rail car, was actually the map of the Chicago Transit Authority (CTA) with the color of the lines altered. The train being filmed was also a Metra train, an entirely different rail system, which features no maps at all in its cars.
Vera Farmiga stated that she took the role just at the start of her pregnancy in February 2010. She knew that in that scenario she would be unavailable for the next 10 months. She filmed her scenes in 10 days.
During Max's stand-up routine, his punchline includes the names "Barack" and "Michelle". Before becoming President, Barack Obama represented Illinois in the U.S. Senate. The film's setting, Chicago, IL was where he lived when not in Washington, DC.
Originally, it was planned to use an actual train station for the scenes off the train, however the place changed terms at the last minute so they had to come up with an alternative, they ended up building a train platform in a parking lot.
Because the owners of the actual commuter station they planned to film in changed their terms at the last minute, a fake station had to be built in a car park. That meant the white van couldn't be prepared in time. The contents had to be simulated using CGI.
This film contains several references to the two movie versions (1962 and 2004) of Richard Condon's book The Manchurian Candidate. In both The Manchurian Candidate and Source Code, a main character is a decorated U.S. military veteran who has returned stateside but who is (without his knowledge) still being used as a tool in a secret military program. In both the book and first movie version of The Manchurian Candidate and in Source Code, the man is "triggered" by a code involving playing cards, and in both cases, a queen is the suit used prominently. Two of Source Code's main actors (Vera Farmiga and Jeffrey Wright) also had prominent roles in the 2004 film version of The Manchurian Candidate.