Answer: It sounds like you are describing blossom end rot which occurs at the end of the tomatoes (and peppers) opposite the stem. While it is attributed to calcium deficiency in the soil, it often appears in cases of fluctuating soil moisture levels. Remedies include adding organic matter to the soil to increase its moisture holding capacity, keeping the plants evenly moist, using a mulch, and in some cases spraying plants with a blossom end rot spray (contains calcium) which can usually be purchased from your local garden center. Usually, more attention to keeping the soil evenly moist will solve the problem. You might want to dig down into the soil a bit and see how effective your watering actually is, or isn't. You want to keep the soil evenly moist, not soggy sopping wet and never allowed to dry out so the plants wilt. With containers, this can be hard to do, especially if the pots are relatively small, the weather is hot or windy and the plants are big. You may need to water twice a day to keep them hydrated. If you think your watering regime has been adequate, then you might try the calcium spray.
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