What makes you think he saved the train in the original universe/timeline?
From my understanding the source code program works a lot like time lines in "Back to the Future":
Colter Stevens' consciousness is being projected through a black hole into a parallel universe, where everything is the same except that he is in the body of Sean Fentress now. By that projection (into an earlier moment) the timeline in the alternate universe starts to differ from the original one with everything he does. The original universe is unaffected by anything he does back there.
When he dies (and he dies every time if you watch closely), his mind is transferred back to the original universe. So when he does not die in the ending, he remains in this alternate universe and in the body of Sean.
The fact that he actually stopped the train does in no way carry over to his original universe where the explosion already happened. What we see in the ending, the pizza delivery and the email being received by Goodwin, happens in the alternate universe, where he actually started those events.
So in conclusion: Stevens does not actually time travel (within the timeline), they just create a parallel universe of an earlier time when the train still existed.