Your picture is blurry, but if the rot is at the bottom aka the blossom end it's blossom end rot.*
You could try watering with a tablespoon of milk in your watering can.
I'd love to know what your eco-friendly fungal/pesticide is.* I'm always anxious to learn about products.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.