However, starting a build should move any NPCs, creatures, items, etc out of the way just before you finish the startup procedure. ALthough if the builder is building another facility I don't think he will move.
Thanks Elias, the builder was building another facility. Firing him worked. I thought he would have moved when I started production but I guess the rules only mean if he isn't engaged in building and is just standing there.
It's who you surround yourself with, that defines you.