I have 2 bell pepper plants that are in pots. They are both strong and healthy plants, but the peppers off of one of the plants always have brown "rotten" splotches on them. The other plant produces healthy fruit. What might be wrong?
The only pepper disease I know of that attacks the fruit and not the leaves or stems, is blossom end rot and that always show up on the bottom of the fruit. It is caused by a failure of the plant to uptake calcium. Even if the mineral is abundant in the soil, uneven watering or a soil pH imbalance can make it unavailable to the plant. If that is what your peppers have you can buy calcium preparations that you can foliar feed to the plant. Nothing you can do for the infected fruits, but calcium may help oncoming fruits.
Although Sunscald is not a disease it can cause tan colored, thin skinned patches on peppers that later will start to rot.