This is what thought about the movie:
1) The source code is a program, but the movie didn't mentioned anyone experiencing the effects on a person besides the protagonist (capt stevens)
2) Steven noticed there's a subtle difference in each source code "re-enacments"
3) Before he died in the real world, he saved everyone in the "alternate" reality in the source code
4) Goodwin pulled the plug at the 0:00:00 mark at the limit of fentress short term memory
5) Steven died in the real world but his conscious continued in the alternate reality and still occupies fentress body (poor fentress, but hey everyone lived right?)
6) Technically Fentress is dead if it weren't for stevens help anyways...that might be an issue, hey ! he got to live to text the alternate Goodwin about the source code success
7) Oh shit , sequel?