I've been playing along all tickey-boo and when I went to look at a youtube HOWTO (Wrecking Ball, grrr) I saw on the region map a Blue zone. I vaguely recall at the beginning of the game the CIA woman (or was it the swede) mentioning a 3rd faction but I didn't think much of it. Now I'm wondering if it's going to be borked (e.g can't get 9 strong holds, etc). At this point I'm almost 20 hours in so I'm not going to start over again but it'll definitely kill my desire to work on side missions for completion %.

Check your PDA map for that faction's first stronghold mission, it should be there. If not, you're fucked.

It's there, I had this same issue.
 
it's on the inner coast, the north most of the three that were originally there. It's hard to see, on account of it being blue, and most of the icon being in water, but it's totally there.

Yep it's there... if it's the blue one it's just a bugger to see. You might just have to find a map online and follow it.  Or go to the house where the Swede drops you after the Casino Mission and follow the coast North for a few kilometers till you reach a mansion.

The Roaches you mean?

The blue faction is the Roaches, if I'm not mistaken. I recall their first mission being somewhere off near the city, though that was some forty hours of game-time ago, and things are a little hazy.

Hrm I'll check it out when I get home from work. At first I thought it was some sort of manufactured re-playability function (more missions for one faction = less of the other).

Yeah it's there you just look for it to be blinking.

 
3RD FACTION COORD X 12744 y11803 hope this helps its somwere there