I believe there's an issue in the train logic here, it could decide to move 1/2 a wagon forwards. I guess in this configuration it takes the same amount of movements, so perhaps it isn't a bug? It seems unexpected to me that it does it though, it could line up two in that step without any issues while it only actually lines up one. My fourth image is a drawing i made to maybe make it a bit more clear.
Another thing I'm not sure if is a bug is if i dont put the dirt and rock filter on the third wagon, it partially fills one container of the wagon with dirt and then leaves the station, it doesn't pull forward and fill the other container in that wagon.
after this it will move forward half a wagon, do nothing, then depart, leaving the final container empty
Just to make sure. you don't have a "forking junction" too close to the station's exit, right?
No, its just one track with no branches all the way to the next station