The actual train changes several times. In the beginning it has a red engine with the number 566; during the ride it has a 1212; when it stops to pick up Chief Walker it's an Amtrak train; at the conclusion it's pulled by a yellow Sante Fe engine.
The train keeps changing! The engine changes from a squarish blue and yellow Santa Fr freight engine, to a streamline Santa Fe "Warbonnet" one (silver with red & yellow), among others. The train cars switch between plain silver, and Amtrak silver with blue & red stripe. It's laughable., and distracting.
The train is supposed to go from San Francisco to Los Angeles. This is not possible. You would catch the train in Oakland and travel south through San Jose. This train made a stop at Madera and Fresno. This is not possible on the coastal train route, as both these cities are in California's Central Valley. If the train route went through these cities, the passengers would have had to start in Sacramento and would leave the train at Bakersfield to take buses over the Grapevine, through Tejon Pass, as there is no direct track to LA in the central valley.
The train is not necessarily a factual error. If it were a Santa Fe train it would have left from Emeryville (not Oakland) and traveled the valley route. If the train were a special, as the story implies, the train could have started in the SF station, crossed over to the East Bay at Palo Alto or San Jose and followed the San Joaquin Daylight route through the valley.
Although the continuity is wrong, the train would have changed/added locomotives to cross the Tehachapi mountains.
In the beginning, Mildred tells Mac they need to be at the train depot in 12 minutes. Since SF doesn't have a train depot (the Caltrain station only has tracks from SF to Gilroy, a town south of San Jose, CA) they would have to catch the train south in Emeryville or Oakland. On a Friday night with typical rush hour traffic, it would take 45 minutes to an hour to get to the station.
In the beginning of the story, Mildred tells Mac they need to be at the train depot in 12 minutes. This would be impossible as there is no train depot in San Francisco. They would need to go to Oakland to catch the train south and it would take more than 12 minutes to get to Oakland. The only train you can catch in San Francisco is the CalTrain which is a local train service from San Francisco to Gilroy, a city south of San Jose, CA.