One of the latest updates added the ability to select which cargo the cars can carry, open wagons for example can carry coal, or iron ore. You need to select which one you want now, no more auto selection!
So if you have a train going from a coal mine, to and iron ore mine, then a steel mill, you need to make half of your train coal, and the other half iron ore. This is done via the buy vehicles menu, when you select the open wagons, or whatever, there a little icon to click on its stats page to select what cargo it will take.
Same goes for cargo trucks.
Hope that helps!