Black spots

First up, I'm also not really sure what could have caused this. But here are my best guesses. 1. Some kind of deficiency? - I'm not sure what type of nutrients you use, but due to the yellowing of the leaf-tips the plant is telling us that its having a problem. And in some cases with late stage deficiencies, the plants develop brown spots on the leaves. My best guess would be magnesium, potassium or phosphorus. Also, the roots are underdeveloped for a plant her size, which could also indicate limited nutrient uptake and therefore lack of nutrients. 2. Mold - Due to the high stress the plant experiences during cloning and the high humidity in your tent, it's not unlikely for mold to appear. Honestly in that case, I would count my losses and chop her down or at least move her out of the tent and treat her with anti-fungi sprays. 3. Her size - She is quite small and she has to recover from her cloning. If the new leaves appear and don't develop these spots, you should be alright. Conclusion: If the spots don't spread, I would probably wait for a new set of leaves to appear and then chop the old leaves with spots off. Or you could just chop them off now, if you want to be extra careful. Sure, chopping them off is more stress for the plant, but if its really mold, saving the plant is more important than having her start with "only" 2 main leaves.