In footprint QFN64_Energymicro there are separate pads for copper and paste, that is there pads with just the copper, and another set of pads with just the paste. Normally in KiCad each pad would have copper and paste defined in the same pad.
It appears FreeRouting does not like the "paste only" pads. I suppose a workaround is to use a footprint from the KiCad library.
I am guessing the footprint was imported from Eagle?