Issue is likely do to having multiple trains on the same track. When a train starts it's route it changes all switches along it's path. So another train on the same tracks will likely have it's engine go one way and freight cars go another. Depending on timing it may even slit a group of freight cars in half routing them opposite ways. This issue is currently making the sharing of track segments with multiple trains a big issue. Technically it continues to work, but agree visually it is bad. I have dozens of freight cars running by themselves it all sorts of random directions.
