I'm not familiar with Trainz Driver Edition but assuming it's similar to TRS2006, on which it is based:
You can drive a train yourself, or you can set up one or more commands in sequence to make the train perform operations by itself.
When setting up commands, left-click and don't hold down SHIFT or CTRL - as far as I know (experts correct me please if I'm wrong).
Getting the commands right can be tricky sometimes, especially when you want a train to go by a particular route and there is a choice. Also, AI (artificial intelligence) trains can sometimes drive past red signals and then carry on as if nothing had happened.
If you're driving yourself, in some industries you need to stop for the wagons to be loaded or unloaded, while in other industries you have to keep moving but very slowly. Industries with more than one input and output have separate sections of track for each.
Industries will only load or unload appropriate types of wagons, the wagons must have the green IND tick in their icons. In addition, industries will only load or unload when it makes logical sense to. For example they will only load when they have some product available and the wagons aren't already full. The will only unload when the wagons have some product available and the industry input isn't full.
There are two driving modes, DCC which is simplest and CAB which is most realistic. In DCC press the > key to go faster forwards, < to slow down and go into reverse, and / to stop.
You can change the junctions by clicking on them. The red and green arrows indicate their directions.
Sorry if you already knew all that.
Is this a general problem, or does it only happen on one route / and maybe one specific Driver session for that route? If so, tell us which and if relevant where you were and what was happening when it failed (unless it failed completely no matter what you tried right from the start.
HTH, John