The interesting question is how you created the STL. Here is an STL I created using your model:
File -> Export.
Your model behaves like mine.Here is an STL I created using your model: case (Meshed).stl
I have printed it. It was fine.It works fine for my 3D printer.
See a picture below...From the PartDesign point of view, your model looks good.
These are just display artifacts. They occur with certain settings. For me it often helps to use e.g. 51% transparency or to to try out if in the preferences -> Display the option "Use OpenGLo VBO" improves the situation.
Now I don't understand you. I just said that you should use the Mesh workbench to create the mesh because there you can adjust the mesh parameters like the maximal angular deviation from the original object. The better the mesh the less the display artifacts.