1.Civilians run away from ALL foreign sensors, because you can open fire on your allies(or anyone at all, for that matter).
2.I'm not sure what you're asking here, but civilians, if not carrying out a contract, will automatically move trade goods based on demand and supply. The start and end points need not be the same. In a multi-faction Earth start, yeah the freighters will pick up goods from the earth colony of, say A, and transport them to the earth colony of B, which is on the same planet, earth, and thus, the freighter doesn't exactly "move" from the planet.