Fab subs don't seem to be counted as fabbers by the game - selecting all combat units selects them, and they (s0metimes) aren't selectable as idle fabbers.
Sub everything still needs lots of work. Since sub fabbers aren't actually submersible, they aren't worth it. Still probably worth reporting on the tracker. http://pa.lennardf1989.com/Tracker/
If you're spamming naval fabbers they are worth it - They are more efficient than surface fabbers... so if you are using 4 fabbers or more on a project you should consider using submersible fabbers instead of surface fabbers (Energy cost is 6175 for 3 sub fabbers and a ship fabber vs 7600 for 4 ship fabbers.) It's kind of odd that they are counted as combat units though. That's the real bug here.
That is a strange bug. I've also noticed that sometimes, not all the time, Commanders will get selected in the combat units. It's really sad, but I've seen players lose matches due to a commander heading off towards the enemy along with a frantic defense. Or Commanders randomly just walking off in random directions out into the middle of nowhere.