The conflict is simple yet difficult to imagine.
Basically, the game functions on a tile grid where each tile is a square. However, the images in the game are rendered with an orthographic camera under 45 degree angle.
We use axis X to be horizontal, Y and Z vertical. This means that everything that is in Y or Z is distorted by square root of 2 - a flat plane on the ground will have dimensions X=1, Y=1.41, and look like a perfect square in the game.
Generally speaking, this conflict results in some perspective magic that vast majority of the graphics have to do.
As a quick nightmare fuel: Anything you see rotate (except biters, car, tank, and combat robots), is not actually just rotating in the 3D space of Blender, but some additional tricks and modifications are happening to it, often times different rotations are using a very different 3D model.
However, specifically rails are weird because they have the conflict directly in them.
The rail metals are made to appear as if they were top-down. Try to rotate the screenshot from OP by 45 degrees in an image editor and you'll easily see all the rail metal lines are horizontal or vertical.
The rest of the rails are done in the 45 degree camera perspective graphics generally use. And specifically the wooden ties use all sorts of weird angles to help the optical illusion that everything is fine.
TL;DR the top sections of the rail metals are perpendicular, but everything else is skewed