That is strange seeing as how I only changed the PCB image and left the other views as is.
But upon further inspection of the pictures I posted above I can now see that they are not connected in the original sketch and are the cause of the original warning. It looks like this pins are supposed to be ground pins. I would just draw a wire in breadboard view directly to your ground rail and ignore the fact they do not line up.
I do not use the breadboard view at all and never make svgs for breadboard so I can not be of much help in fixing the part to line up.