Sketchup Free STL import in FreeCAD not working with Fasteners Workbench
Stls may not properly import as solids.  This is likely what is happening in your case.  Stl format is ultimately just a bunch of triangles without a proper definition of a solid.  The boolean Difference found faces to attach to the circle so it used them.  The trouble is, there were even more faces at the same location (not uncommon).

You could manually delete and repatch the triangles in Mesh Design or if the shape is simple enough (I think your box fits the bill), redraw it.  I don't know how far sketchup has come with file formats, but a different format may convey your solid better between software.

That said, in your shoes, I'd be making cylindrical and hexagonal cutouts and gluing a nut into my part.