The Enslaver plague. The C'tan really don't like warp energy, and when psykers started collapsing the barriers between our universe and the warp at the fall of the Old Ones, and the birth of the Chaos gods, the C'tan and the necrons went into hibernation to let the Chaos pass.
That's fair enough in itself. But I meant why haven't they wiped out the galaxy now that the danger has passed and they've awakened once again? It's essentially the same problem as 'if the Empire can build Death Stars so easily, why does it never build more than one?'
As I attempted
to say, the new arrangement works well in that the C'tan are currently limited in their power to the point where the problem does not arise, but at the same time their original power is retained by implication. Before being shattered they were unstoppable godlike beings who did
pretty much wipe out the galaxy and were a credible threat to the Old Ones. One of them, Llandu'gor the Flayer, actually managed to inflict the Flayer curse on the Necrons in its final moments, and said curse is still spreading to this day in the form of the Flayed Ones.
Also, I was interested to discover that the Silent King has returned and is gathering Necron forces to fight the Tyranids (perhaps kicking himself for destroying his command codes). That provides a convenient explanation as to why the Tyranids haven't wiped out the galaxy for that matter, because the Silent King has been actively intercepting at least some of the Hive Fleets.