Answer: Squash can suffer from blossom end rot (BER) causing them to rot beginning at the bottom of the squash. This is related to uneven soil moisture levels. Make sure you are watering as needed to supplement rain so that the soil stays evenly moist like a wrung out sponge, meaning damp, not saturated/sopping wet and not dried out. Also, using an organic mulch will help keep the soil more evenly moist.
I am not certain what you are seeing in the soil. You might want to check with your local county extension to see if they can help you identify those.
I hope this helps.
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