Answer: It sounds like you are talking about 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.
With regard to fruit being malformed or failing to form, there are many variables which can affect them. Most common are probably incomplete pollination, uncooperative weather (too hot, too cold, too dry, too wet, too windy, too changeable), insect feeding damage and finally, soil problems/deficiencies and insufficient moisture. If a plant is stressed it may drop fruit or "stall" or develop poor quality fruit. I hope this helps answer your question.
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