You should not be feeding them layer feed at this age at all. They need higher protein to grow. The guidelines on the backs of those bags are for chickens, not guineas, and even then I don't think chickens should be on layer feed at 12 weeks old - a good two to three months before they will start laying.
So your protein is way too low, and your calcium is way too high. You've been feeding them food that contains way more calcium than they need. Too much calcium causes liver and bone damage, kidney failure, and, eventually, death. Switch them back to a grower feed with more protein immediately.
It might not be the feed causing the issue, but from what you're saying it's the only problem I can see in your husbandry, so short of a disease I'm not sure what else could be causing this. Is it possible they're getting into and eating something they shouldn't be while free ranging? How does their poop look?
You should also be leaving feed out free choice for them so they can eat as much as they need now while they're growing.