It seems to me, to be totally reasonable that not all galactic clouds would form into full galaxies, complete with stars and planets.
Not to me
The reason stars and planets exist is because of gravity. Everything is subject to gravity (unless you start postulating about things with negative mass etc. as mentioned above - but even they are affected by gravity in a different way). two particles of dust 10,000 light years apart would (assuming no other gravitic influence) eventually collide - and yes it would take a *very* long time but it would happen.
So, if you have a cloud of any size, it's going to start condensing, and when matter condenses that way it either forms balls of stuff (like Jupiter if the matter is hydrogen) or goes further, gathers more mass, until the critical point is reached where it begins to collapse in on itself under its own weight. After that, fusion is a short step away, which continues until the fuel funs out. At which point boom, hello nebula, rinse/repeat.
Eventually, there will be no more fuel, and when that happens, the part of the universe's history where there is light will be over (except for white dwarf stars, the superheated cores of stars which ahve gone nova - our Sun will form one when it dies). But the universe will persist for billions and billions of years - the stellifferous (or starry) part is estimated to last maybe 150 billion years, but the dark part of ths history will be many, many times that long.
Gotta love entropy, one of the most depressing forms of inevitability there is.
But what that means is dark galaxies = not happening unless the material they are made from is exotic in ways even theoretical physicists on LSD have yet to comprehend.
But all is not lost. The concept of a dark nebula, which is full of particulate matter and gases far beyond what is normal for interstellar space, and which is dark simply because you can't see into it, is well established. You could easily hide a star cluster in there from which the bad guys originate - especially if the nebula had somehow engulfed some habitable worlds along the way - and the nebula's particulate mass makes it very dangerous to navigate (the bad guys have some kind of super-shield that lets them fly into it undamaged)...
