I'd have the Primaris marines develop some kind of unpredictable degeneration or instability, unforseen by Cawl; perhaps the Bellisarian Furnace starts activating at random. Then maybe have Cawl killed off, or have some person or group attack him in a way that causes him to lose the knowledge of how to fix the problem.

This would mean chapters need to weigh up the benefits of going Primaris. Do they want to carry on with the risks, or revert to creating only Firstborn? How will it affect the logistics of the marines, knowing they're going to be losing members more often - does recruitment ramp up, resulting in less suitable recruits chosen? Which if the main characters falls to it, perhaps even dying off the battlefield with no warning? What rituals and customs does it create for the chapters, such as a marine feeling it coming on and going beserk mode as he knows he has only a few days to live? Does it turn the Marines against the Mechanicus, or at least make them less trusting, because they were promised this new technology only for it to turn out to have serious risks?

As an alternate to this, perhaps it could be some latent scrap-code virus introduced into the new Primaris equipment by accident during Cawl's project (e.g. infecting the weapons/armour/vehicles/etc). It could have a similar effect overall, making guns liable to randomly jam or vehicles that respond poorly to operator inputs.