Not sure what damaged plants
I have googled and looked up but I cannot find this issue anywhere. I noticed fungus on my garden plants, which took me by surprise. The same day, I found mushrooms growing in the garden and I disposed of them. Of course, I had to trim what was effected. The next day, there were a few that were see through. I can see the top and bottom of plant but it looked as if there was no chlorophyll in that one part. Please help me identify the issue! Backstory: 2nd year organic gardener. I have been using neem oil. I ran out of neem oil & I had to spray my garden after an warm evening rain. I went to Lowes and grabbed the "neem oil" that they had and this is when everything started happening! I went to the hydroponic store today (the only place in Jacksonville, FL where they sell 100% neem oil!) and I know it will help with other issues that came up after using Lowes' supposed neem oil (such as an increase in leaf miners; *insert eyeroll*). But I would really appreciate help as far as the section above.
I am not sure about all the factors that have resulted in your plant disorders. Growing conditions, soil fertility and water management are the foundation of plant health. Biopesticides can be an important part of your plant health care program, but look first to the cultural management. Mineral balanced, high humus and organic matter content soil will build plant resistance to pests and diseases.
Regarding neem products: The Lowe's Garden Safe brand (70% clarified hydrophobic extract of neem oil) is an excellent product and would be my first choice. It is an EC (emulsifiable concentrate) formulated to mix well with water. 100% neem oil does not, so you may get concentrations of oil depositing on the foliage, which can cause burning. With the 70% neem oil, mix 1 oz (2 tblsp) of the concentrate from the jug, to 1 gal of water. Spray every two weeks for preventive action. Every week if you perceive high pest activity. Neem should not be thought of as a cure, but a preventive measure. If you have an advanced pest infestation then a different biopesticie would be more appropriate for knock down, like a pyrethrins (pyrethrum, chrysanthemum extract) 'Evergreen Prethrum Concentrate' from http://www.domyown.com.
It appears that your plants have some fungal leaf disorders, but that may be burning from excessive neem oil, especially if you are mixing it in higher concentration than the label rate or using it too frequently.
Leaf miners are tricky to control, because they have an adult moth phase, eggs and then the larvae that do the mining and damage. You can't control the larvae with neem or other external spray materials. You have to prevent the adult moths laying eggs, and that is where preventive, repetitive neem oil applications would be useful. Otherwise you need to use a systemic insecticide to get to the leaf miners where they are feeding. Systemic insecticide is not appropriate for food plants.
Hope that helps, Don