probably fungas. I got rust fungas from clones as well. Not pretty. There are a couple of sprays, treatments on the market, but they only contain it, not completely eradicate it. If I where you I would consider ditching the clones and keeping a close eye on the remaining ones.
I say that because my entire grow now has it. It doesn't kill your plant, unless you ignore it and do not treat, but I have to spray once a week, religiously, and I do loose some fan leaves to it. I have to just cut the leaves off that show signs of it which leaves the plant with less leaves to photosynthasise (sp) with.
Spectraside and green cure are two fungasides that I use.