Hi Sarik. I found a reference that said bottom rot on peppers is likely due to Calcium Deficiency from lack of calcium in the soil, over watering, or mineral imbalance (excess sodium, nitrogen, potassium in the soil). But I am not familiar with your style of growing, so I cannot offer suggestions. Hopefully others in this forum can help.
Take the Bottom End Rot (BE?r) fruits off, water with a bit of Epsom salt or milk or anything that gives your plants calcium. Don't let the plant to suffer before watering nor over water it during hot spells.