Not a bug, a feature the female pins are whats on the breadboard in breadboard view. They don't by themselves connect to anything they just facilitate connections between other parts. I think (but I'm not sure) in your case they were used on the screw connectors so (possibly along with the hybrid key word) they don't show up in pcb view as the screw terminals aren't usually accessable from the pcb.
I agree, that's why I was lazy and didn't try and do something about it (and because there are translates in the svg which make changing the hole sizes much more difficult). Good job, hope you do some more