Cura imports FreeCAD stl wrong
I suspect that your method to create the hole for the pins may not be consistent with the modeling practice that FreeCad and other programs of this nature require.

Consider the following:

Import your base shape.
Create a second shape that matches the hole you wish to create. It must be a solid object, not a plane or other single surface item.

Consult one of the many FreeCad tutorials that present the method to use next, that is to place the shape to be subtracted in the desired location, then perform a Boolean operation involving both objects. In the linked tutorial, it's referred to as a cut, which is an accurate description.

Performing this action will create a surface where the two objects intersect, removing the smaller one, leaving a solid, rather than a zero thickness surface. 

You would then create and place the cylinders in a manner consistent with the original model.