what and how does a system quarantine happen? is it related to the fabricator check network (which I don't get either)
Hm, no one else seems to have fielded this, but this is just something that can happen if the system detects something is amiss, nothing you can do about it but leave for another area.
Does it effect me? ???
I assume you're talking about the fabricator quarantine. Yes, it locks down all the fabricators on the current map so you can't start anything else. (If a fabrication is already in progress I believe it will finish normally.)