[Alex]

I thought about it a bit more and it may not be the issue I thought it was.

Spoiler:

My initial understanding of was was happening is that every time Source Code was invoked it spawned a new parallel universe, created entirely by Source Code.

So the question was, how did Source Code know all of the stuff outside of the direct experience of Sean Fentriss such that it could be used to accurately mirror what was had happened in the real world.

In other words, if all of that information is already in the computer, there should be someway to query it more directly.

But instead, I think it is correct to say that without the program people understanding it, they were actually injecting just him into the alternate reality that was, because it was forked from their specific moment of reality accurate.

So the movie explains it, but the movie doesn't explain why the scientist guy would think what he thought was the way Source Code works, since that doesn't make sense.