Go through your system and double check things are in place and working properly.
Rust is an air borne fungi. if given the opportunity, it WILL take hold. it usually does during flower as this is when the plants immune system is at its weakest as its energies are concentrating on re-production, not survival.
depending on what part of the grow you get it, you can cure/minimize it with either chemical or natural remedies.
it enters the leaf via the stomata and then it's off and running.
fungacides used are generally copper based and include; thriram, manzecob, maneb or zineb at 10 day intervills.
organic;
baking soda, 1 tea spoon/ quart of water. spray on.
copper sulphate, read lables.
fungacidal soap sprays;
garlic sprays, 1/2 cup minced garlic, 1 quart of water. let sit 24hrs, strain, spray.
sulphur, one of the best natural sprays. it is low in toxicity.
micro kill, a citric based killer has great sucess.
If my answer helps you please pick it and save your crop please, dont mess with soil, mess the fungus intead.
Good luck. Hope you help back for the grow questions contest, its just picking one answer and you help me or anothers.