A brown depression on the bottom of tomatoes is usually blossom end rot (BER). This disorder is related to a calcium deficiency aggravated by irregular watering. Since most soils have adequate calcium, watering is usually the problem. Without regular watering, the calcium in the soil cannot reach the plant. Mulching can help. Water tomatoes regularly. Avoid flooding them so the roots sit in water. For more detailed information about BER please view Managing Blossom-End Rot in Tomatoes and Peppers.