My Thoughts

Colter gets sent to an alternate timeline each time he re-enters the source code. The ending of the movie when Colleen gets a text is a Colleen from the same alternate timeline as the last time Colter went back(when he sent the text). It had been shown in other shots that Source Code goes longer than 8 minutes which I think is linked to the head honcho’s speech about the brain still being on for awhile longer after death, this is shown Colter is able to witness the train exploding and keeps going, but he always dies through another event. It helps to explain the movie and why Colter keeps going even after the 8 minutes and the pause, I assume that once his brain is fully dead Colter will no longer be in Shawn’s body and will be brain dead. Shawn will return back (as in his consciousness that Colter overtook) and be confused as to why he is now off the train with Christina and they are now in a relationship. Also there can not be 2 of the same person or thing in an alternate reality as it would create a paradox, akin Back to the Future or Donnie Darko. That is why Colter's real body exists in the Source Code facility(from the alternate timeline) in the end while Colter's Consciousness from the original reality lingers in Shawn for those final moments. Physical Colter exists in the Source Code facility while Conscious Colter exists in Shawn for the moment. That way both Colter's can exist from the same timeline