Sorry for chiming in so late but I only watched Source Code today.
I admit I have some trouble following Film Syncs' argument. Here's what happens according to me:
Colter is being fed with Sean's memory. As soon as he starts interacting with the passengers he is creating a parallel universe where things play out differently. That's as far as suspension of disbelief has to be stretched. After the 8 minutes Colter reports back to Universe 1, so they can take actions to prevent the nuking of Chicago.
The lab executive explicitly states that the Source Code opens up a parallel universe. At the same time, however, he denies to call it time travel which is the only flaw I see as they actually do go back in time - but it's no biggie in my book. Anyway, neither of the characters nor the audience is being deceived with what's happening. The crew just couldn't be bothered with the outcome of the alternative universes.
One disagreement that actually happens to exist between the characters is the idea of what's happening to the alternative universes after the explosion and the death of the remembering mind. The lab crew seems to believe that this will bring the alternative worlds to an end while we are told otherwise. Again nothing to be concerned about. Some actually call it the twist in the movie which I feel is giving it too much credit.
So what's the fuzz about - am I missing something here?
I was actually more concerned with the happy sappy ending they pulled out of the hat. The director had more guts in his previous work Moon …