I initially deleted all the items on the layout, so all I had left was the page outline.....the lines remained in 3-d.
I then deleted the pcb file, and vreated a new pcb with nothing in it, and the lines were gone, but the 3-d had other stuff, that obviously should not be there.
Creating a new project with an empty pcb shows as it should with nothing in the 3-d.
Here's the pcb file with the junk lines.....without external footprints, it might show correctly.
nanominilayout.kicad_pcb (100.5 KB)