Scully says that if the train explodes with the guy inside of it that the disease that 'they' infected him with will spread quickly over a large radius.

So does this mean that when it exploded that the spreading occured?

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This should probably be asked in the previous ep but why does Mulder jump onto that train with his phone still in his hand? Not only does this make a solid landing more difficult but it also guarantes him dropping it, which he of course does.

Since there was no outbreak of hemmoragic(?) fever it should be quite clear that Mulder's theory on what was in the train car was more accurate. Granted the car was deposited in "as isolated an area as possible" but it was still an active line with another parallel to it and buildings in the background. Either way, how isolated could this area possibly be? On the other hand, I wouldn't think an outbreak is at all plausible when the carrier is destroyed by what appeared to be an incendiary/C4 judging by the explosion.

I may be wrong about this but I highly doubt Scully could drive from rural WV, to a senator's office in DC (she mentioned going by Matheson's on the phone), then to Mulder's apartment, and reviewed his autopsy video getting the exit code all under 1:40.

She was using Jack Bauer's magic freeway from 24.