Has nothing to do with Alternate Universes
Nope, I can't believe that Source Code not a simulation of Sean's short term memory track, because that's how they programmed it. Its just a computer program, and computer programs do not make alternate universes.
The only reason to believe that it actually created alternate universes is that his simulated life continued on after his life is terminated, meaning a universe must continue beyond this computer simulation.
This can only be explained by:
1) Plot hole, thus inexplicable. Director just trying to make the movie more complicated than it is, and in doing so it allows for viewers to make their own conclusions about the ending, just as we are right now.
2) "The brain is like that. It's electromagnetic field remains charged just briefly even after death. Circuits remain open."
This is a quote from the movie from the Doctor as he explains how the Source Code can work. Just like they are using Sean's brain and memory after he is dead, Colter's brain and memory can still continue on even after life is terminated, but only briefly.
3) The entire movie has some supernatural, external forces - such as Fate. In the last scene, they visit Cloud Gate, the reflective sphere thing. So this alternative universe ending was fated to occur, in which case I will believe alternate universes happened (albeit supernaturally).