Now that I've seen it, I agree with Michael and Trey that the only way the ending and much of the rest of the film make any sense is if the machine is more than an 8-minute simulation created from the brains of the dead (whose brains wouldn't be in good shape anyway after being on an train traveling 45 MPH and exploding).
But for that to work thematically, Jake has to SAY, "This machine isn't what you think it is. I can CHANGE the past." Then the scientists need to go, "Tut, tut, brain in a jar," and then privately say "Is there something TO this? We really DON'T know much about Doc Brown's flux capacitor before he died."
Boom. Movie fixed.
EDIT: To clarify, it is a strong rule of storytelling that anything that an authority figure like a scientist says is true unless it's questioned by the protagonist or antagonist. (It's how "the rules" get delivered.)
But in thrillers, where the main theme is usually "all is not as it seems," you need to be able to subvert the authority (who is usually a lying baddie). But any other character questioning the authority is usually the "Guinea pig". He's the guy who says, "You're full of it," walks out and gets eaten by the aliens or zombies or whatever to help prove the authority correct.