map2dif orphaned polygons

I'm using valve hammer (world craft 3.4) to create map files of buildings. When I convert the map file to dif with map2dif the output says I have orphaned polygons... and lists it as an error. I have two cubes one for the building and one for the ground at the base of the building. They are right next to eachother. Do I need to link them some how? Is this a real error? It seems to work fine when I use the dts file in game.