@User: I'd have to know what you're extracting and how you're doing it. There are several ways for this to happen, most often with "abstract" views of cells, where magic doesn't really have any idea what's going on inside the cell. But this can also happen with floating metal, and would indicate failure to connect the metal to something. If the floating nodes seem harmless (note that true floating nodes are prohibited by the DRC rules, although I consider that largely unjustified), you can suppress the output of them with the "-F" option to ext2spice.