There are 1 or 2 bugs that may or may not be related to one another (I'm guessing they are).
1. Dark Inquisition (and perhaps other guilds) are able to issue a guild command on a region that is not connected to our other regions (see here: http://prntscr.com/2znup9 our regions are in the South, but we are able to issue a command in the Temple Region in the North)
2. Meanwhile, Blackwater is unable to issue a control command on that same region, which IS connected to their other regions (Naz will hopefully post more on that if needed.)
(Edit: seems he did... http://www.battleconforum.com/t2067-cannot-lunch-a-warfare-command-on-r45#16024)