Your roots are lacking proper oxygenation. When the plants can't get enough oxygen in the root zone the result is build-up of bacteria, fungi, and mold on roots. If you notice the brown spots are where the plant sits in a flood area in the pot so to speak and that is where it spreads. All the roots above the flood area are pretty white but, where your plant sets in water for longer periods of time, it cuts off the oxygen. It will spread to the healthy roots once it changes to fungal disease, anthracnose and cause harm to the rest of the roots and yield.