Boy, you DO have a problem... without a diary, I can't really tell much of anything here - but your description of the spots starting to go up the stem coupled with the fact you're growing in living soil has me concerned this might be a fungus.... but that's about ALL I can tell you! I would do some research on the various fungus that attacks cannabis (the only ones I can rule out are botrytis and powdery mildew)... I'm concerned it might be septoria... this article might help you figure out if this is what you're dealing with: https://www.ilovegrowingmarijuana.com/growing/marijuana-diseases-leaf-septoria/ In it, they specifically say septoria (which is also called Yellow Leaf Spot):
"will harm the leaves and often times the stems of the plant, although it won’t cause the crop to die off. If for any reason this is not properly cared for it will lessen the marijuana plant’s yield. The affected leaves will become dry where the spot is and overtime break and produce a hole at the point where the spot started off."
Good luck....