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Train stations apply a heavy penalty to the path length if a train passes through them.
When the path includes a train stop that is not the destination -> Add a penalty of 2000. from https://wiki.factorio.com/Railway/Train_path_finding

Your InternKraftwerk and InternIronWest need to be passed by ...

I think something is wrong about the pathfinding of the trains. Sometimes the train takes a much longer path than the shortest path. It is much more easier to show the issue than to explain it:

Here: Condition.jpg you can find 4 Stations and it is obvious, what would be the shortest path from the ...