The mission involves Stevens trying to find information about a dirty bomb attack on Chicago. A "dirty bomb" is simply a regular bomb with radioactive material packed around it so that the explosion will spread harmful radiation over the blast zone. It is not a nuclear bomb, and while it would expose those in the area to potentially lethal levels of radiation it would not "kill millions" as stated in the movie.
The college kid flips open Frost's wallet and the driver's license is visible. Later when Colter Stevens opens Frost's wallet, Stevens has to slide the license out of a pocket in the wallet before it is visible.
When Goodwin pulls up Frost's driver license information on her screen, the address, SSN, height, weight, DL # and eye color are different from the ones Stevens sees on his actual license on the train.
When Colter Stevens is on the train and makes the cell phone call to Nellis Air Force Base, the voice on the other end says, "Post Operator." If he was calling an Air Force base, he would be connected to the "Base Operator." Only Army facilities are called "Posts."
Captain Goodwin's uniform is incorrect. Blue name tags are not worn on the Air Force service coat. (Blue name tags are only for the shirt, whereas silver name tags go on the service coat). Also, her U.S. insignias are not properly placed on the lapel.
Captain Goodwin has five service ribbons: a Bronze Star, an Air Medal, a Joint Service Achievement Medal, Kuwait Liberation Medal (awarded by Saudi Arabia), and a Kuwait Liberation Medal (awarded by Kuwait). However, she is missing her Basic Training ribbon.
When security personnel are called in, US Army Military Police show-up. Nellis Air Force Base, like all Air Force Bases, is protected by US Air Force Security Forces personnel. Contractors are sometimes used to provide minor assistance such as checking identification at gates, but MPs would not be stationed on an Air Force Base.
The conductor always asks Colter for his ticket, but never asks Christina for hers. On Chicago commuter trains, conductors collect tickets as passengers get on; Colter must have gotten on after Christina.
When Cpt. Colter Stevens finds the train bomb's cell phone which is the remote trigger, it is playing an Adobe Flash file (named "HISTORY.swf"). Even before he looks in the call history of the phone, this is visible.
Christina's hair is styled differently in the last scene in the train and the one immediately after when she and Colter have left the train and are walking together in Chicago. In the train her hair's tips are clearly pointing outwards and in the following scene they are just laying on her back.
When Captain Coulter Stevens has his physical body shown the first time, the EKG electrodes are in the wrong position (white should be on the right shoulder, black should be on the left shoulder and green should be on the lower right limb).
Christina's pose as she says the line about "good advice" changes every couple of Source Code streams. Every sequence creates a new reality, so every sequence will be slightly different - some of the same minor events might happen every time, but in a slightly different way.