When using a base spline that has curves with a tight radius, you get badly deformed geometry and edges that cross over.
This problem occurs when the spline's interpolation value is too low so the geometry is not able to accurately follow the corner. Try increasing interpolation directly within RailClone by going to the Style rollout and adjusting the Curve Steps value.
You can see in the example how this improves deformation.
In order to bend correctly around a corner, the segment's length on the Y axis should not be larger than the radius of the curve, otherwise edges will overlap. The animation below helps to illustrate why this occurs.