When Will and Leo are pulling into the St. Louis yards and they spot the hobo on the track and apply the brakes, there are no train cars seen next to them. When they get off the train to talk to the hobo there is a piggy back train next to them.
In the scene where they run through the police car on the track, first a boom mic is seen on the bottom on the screen, then a dolly track and boom mic again.
The idea that a major rail company would suddenly become an air freight company overnight is completely unthinkable. Railroads make most of their money hauling material in bulk, which includes vast amounts of coal. Not only would coal be impossible to ship by air, but so would other heavy bulk materials such as ore, steel, lumber, chemicals, grain, scrap metals, and even heavy machinery. Railroads excel at moving the most heaviest of goods efficiently and have yet to be proved obsolete by any other mode of transport in this field. The only competition air is to rail is that of passengers and time-sensitive mail and packages, but "Southland" is said to be doing only "air freight."