About the size of your fist... my first guess as to the blackened skin problem would be Anthracnose... a fungal disease that shows up from time to time on riepening fruits... not a lot you can do about it if it is this problem. Pick the unaffected peppers and use them right away.
There's an off chance it could be a bacterial infection that attacks the actual seed which was the source of your plants. If these were raised from seed, be sure to use only approved, treated seeds. If they were plants that you bought, you might at least talk to the plant grower so they will know to treat their seeds.
Best of luck!