Bevel gears 3D model
I don't know how to explain how the problem is occurring with the STL post-processing tools you are using.  

Try loading the STL directly into a slicer and view the result, then slice and view the toolpath.  It is always helpful to eliminate steps in an attempt to narrow down where the problem is generated.

Were I to try to patch the OpenSCAD model, I would create a hub component that overlays where the crack is found.  This would be small cylinder with a hole that overlays the hub.

I have had success adding elements and holes to existing OpenSCAD models and imported STL files using OpenSCAD.