Your finding some eggs in nests, but maybe not all of them.
They are
sneaky hiders of nests, confining them is the only way to be
sure.
1 male should be able to fertilize 12 females easily.
Have read of much higher successful ratios in BY flocks.
Commercial hatchery/breeding standards for fertility efficacy is 1:10.
No guarantees, as fertility has numerous aspects.
Not sure if premix has any of the 'nasties' you want to avoid, but not giving them vitamins/minerals/amino acids may well be part of your production problem.
You might try searching, or starting a thread in, the
feed forum to help balance your birds nutrition.