Hi,
It sounds like the ceiling is in a high moisture environment, like the unconditioned air of a new construction site.
I would guess that the mildew formed due to moisture
forming on the surface of the primer and a lack of air movement in the area.
At this point you need to get rid of the mildew with a solution of one part clorox and four parts water. small areas can be cleaned with a sponge. Rinse well with clear water and let it dry.
I suggest that you topcoat the ceiling with an acrylic paint that has a sheen, perhaps a "satin" or "eggshell" finish.
You might also consider having a mildewcide added to the finish coat, you can request additional mildewcide at the paint store.
Hope this helps
rmichael propainter