If you ever get in ti breeding, runts are normal and are expressions of bad genes in the purebred family. Most strains these days are crossed so many times that they've gone back to their land-race genetics and show all kinds of funky things. I've seen double chromosome buds, hermaphrodites of course are another defect, usually from breeding a hermi'd female with a male permanently soiling the gene diversity of that line. The simple rules go; cull the runts, save the males and stick 'em outside in the elements. Abuse the females a little bit by breaking branches here and there, also oxygenate the soil by pouring high and not over-tending the earth around it by packing the soil and making it too flat/even. This keeps root mold at bay and keeps airflow at the roots like it would in the wilderness. Flower the females, smoke the buds and breed the best female with the most vigorous male that could handle the outside elements. You get 5-star strains this way.
By the way neem oil is harsh as fuck to smoke not gonna lie, have you looked in to natural fungicides using citrus? It doesn't leave a waxy coating on your buds when they flower (that stuff never completely gets off after flushing)