This looks like end rot, a condition that can affect peppers and tomatoes. It used to be thought that this was due to low calcium levels in the soil, but recent research shows that this is likely not the case. The current thinking is that this is caused by stress to the plant from irregular or improper irrigation. Fluctuations in irrigation, going very dry and then being really soaked; shallow watering; or too much water can all lead to end rot. Root disturbance from tilling next to the plants can also be a factor.
The best thing to do is water deeply less often – don’t hand water because people get bored long before the ground is soaked deeply. Using a sprinkler or soaker hose, leave the water on for as long as it takes to soak the ground down 12 to 18 inches. Dig down with a shovel or trowel to test how moist the soil is 18″ down. Irrigate for as long as this soaking takes every 5 to 7 days depending on temperature. Don’t splash foliage or peppers with water in between. If your garden is mulched you should be able to water deeply every 6 to 7 days and have that be enough. If you soak the soil deeply the roots will grow deep and can stand going that long with out irrigation. Read more about this here: http://extension.uga.edu/publications/detail.cfm?number=C938
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