PlantLife Online

Answer

Sounds like your tomato peppers could have blossom-end rot. Blossom-end rot is a nonparasitic disorder that can be very damaging to tomato, pepper, eggplant and many other crops. Blossom-end rot begins as a small sunken dark spot of decay at the bottom of the fruit (The Blossom End) and progresses toward the stem. The decay often begins while the fruit is still green. On peppers the decay may develop on the sides of the fruit near the blossom end and may appear tan and leathery, often mistaken for sun-scald lesions. Blossom-end rot is physiologic disorder associated with a low concentration of calcium. Fast growing fruit like tomatoes require a relatively high amount of calcium during development, when the calcium is lacking a sunken lesion at the blossom end may develop. Once the decay begins other damaging pathogens may enter leading to the total destruction of the fruit.

I would avoid eating affected fruits.