I think you nailed it in your description. It looks like rust fungus. If it is, you will see a corresponding blister (raised bump) on the underside of the leaf. It spreads pretty rapidly. I have dealt with this in the past. I used a mixture of baking soda and horticultural oil. It really didn't seem to affect the spread IMO. Further reading about rust on edibles indicates that the fruits of plants affected by rust are still edible. It seemed to arrive at my last two weeks of flowering. Looking inside my buds I saw no evidence there; I suppose due to the bud cluster being so tight the spores couldn't get in there. It is quite common in the spring on a multitude of plants and trees, so it probably came in with you. It does rob the plant of nutrients. There are a lot of gardening sites online that discuss control.