There does appear to be a problem with the size of the pane separators. I changed their colour to red in order to see what was going on and I could only see the separator between the navigator and the view. Changing the padding and margin make the separator visible.
Try the following css:
paned>separator {
margin: 0px;
padding: 1px;
background-color: black;
}
The easiest way to test this is by adding it to your .config/gtk-3.0/gtk.css
file.