Living soil and rain water problem

Looks like your having issues with some nutrients. I can see Calcium and maybe some Magnesium Iron and sulphur. Living soil is great, however it does need amending or it uses up all its available resources. The idea behind it is you feed the soil microbes who in turn feed the plant, This is believed to have better symbiosis and create a synergy between the plant and its soil and can lead to better abilities to fight off drought and diseases. but with out food for the microbes or the plant it runs out and in a pot this can happen fast. I find topdressing every 3-4 weeks helps but in transition to flower it needs a bit more. and unless the top dressing is getting mixed in well into the top later it is not going to decompose well. Plus if your disturbing the roots this can cause some issues so it almost always better to leave a few inches of head space in the pot so when you do top dress you have room to add in more soil and work in the amended into that new top layer. This is all not needed if you use liquid nutrition as it does not need to be broken down its good to go as is. It also looks like your plants are overwatered. and this can cause root issues that mimic a lot of issues. let em dry out more before giving more water or shelter them a bit if they outdoors, Next year add in more perlite to help it drain more effectively and not get water logged. Rain water is fine and should not be an issue unless you have very acidic rain PH below 5.5 or the thing your collecting it in is contaminated with something like bacteria fungi or chemicals. Good Luck!