Source Code/WMG

This is not the first success of the Source Code project
Fridge Brilliance: Colter actually keeps preventing terrorist attacks and creating new universes where the project was never used. One day the Colter in the new universe made at the end of the movie will be asked to stop another, different terrorist attack and will wind up dead in that universe, having taken over the body of someone in another new universe.
 * Indeed, for it to have worked here it had to have worked before.
 * Why couldn't that have been the first time it was used? However, the guess does give more explanation of what Coulter's body and brain were doing in between his disappearance and the beginning of the film, other than the obvious possibility of nothing.

Colter died, and went to heaven.
Or Hell. Or something else. Take your pick, but he most certainly is dead.
 * My guess is that the epilogue and only the epilogue is heaven... Unless that's what you meant in the first place.

There are multiple Colters in the world
This was just the first one who was either willing or able to get in contact someone at the base.
 * This would have been an especially Mind Screw sort of ending: The "synaptic compatibility" thing is incorrect, and… everyone on that train was Colter, every iteration.

Colter can only exist in one place at once.
Or rather, his mind can on exist in one place at once. When he's send into Source Code, his mind exists there. Once the 8 minutes are up, his mind returns to the "real world", until he's send back again. Once his life support is cut off in the "real world", his mind can only exist in the source code, so he stays, causing a new timeline.

Colter never even joined the Army.
He just started getting really high while he and his friends watched Black Hawk Down. When the film finished, they were a little less high than he was, so they while they watched The Matrix, he started to imagine being an actual Army helicopter pilot. He begins to imagine that he has crashed and woken up in a box full of computers and then that he's a dead guy in an alternate reality machine. The end of his hallucinations meld into a daydream about hooking up with the female friend he has a crush on by taking over the body of her boyfriend.

== The director has no idea what he's talking about and did not invent the components of Source Code, he just worked a misunderstood mental other-universe targeting system thingy into a past simulation. == Designing such a thing, then thinking it does something totally different and having kind of silly Techno Babble to explain it, doesn't seem like the thing the machine's creator would do, even after discounting the Techno Babble from a Doylist perspective. I find it likely that Rutledge was given a Lies to Children style speech from an associate of his who worked in quantum physics and/or bionics, built the thing, then added a bunch of other components to turn it from a What-If Machine into a Mental Time Travel mystery-solving device that the military and patent office considered unique work (assuming he didn't steal it outright).

The ending is in Colter's head.
The source code program is based on using the brain energies of a recently dead person for eight minutes, right? When Colter's life support gets terminated, his brain is still firing for eight minutes, imagining up the end where he and Christina keep living and he makes a difference in the real world. That is why it goes against how the program is supposed to work, because none of it is real.

Source Code happens in the same Universe of Groundhog Day.
It explains what happened to each universe after Bill Murray's mind travels back to the day before, the universe continues without him, and he doesn't wake up dead or anything, he just wakes up as a mind overwritten by Colter (or someone else in the Source Code.)

So, Bill lived the first day as shown in Groundhog Day, then died 8 minutes after waking up by a terrorist attack the next day (say, a nuclear explosion blowing up the whole of Punxsutawney), at that point, the next day his mind is taken over by a Source Code traveler, while Bill's mind is sent to the day before in a different time line (in where he either suicides or dies the next day again, being sent over and over to yesterday.)

Eventually, Bill Murray lives the day so many times that he stops the nuclear attack by accident, his mind isn't taken over, and he can live the rest of his life.

(I know the character is called Phil Connors, but I had to look it up, while everyone remembers it was actor Bill Murray on the role)

Back to the Source Code movie, every time Colter takes over Sean's mind, his mind is sent to the day before, to live the day over and over, he never sees the train explosion, nor knows what happens at the point in where his mind is taken over, it is a mystery. Sean gets stuck living that day forever, or eventually stops the attack by accident (which would mean his mind isn't hijacked), or just doesn't get into the train, at that point he isn't on the train when it blows up, and Colter has to take over the mind of someone else in that timeline (starting the cycle again, until eventually someone is going to stop the attack accidentally for sure, nobody gets on the train, or the attack becomes unstoppable.)