It just happens. Sometimes it's too much/irregular watering (though they're not as picky as toms about it) and sometimes it's a sign of a bug invading the pepper through the flesh. Sometimes it's just how the plant developed that particular fruit and it's simply not as well developed as others on the plant.

The small amount of peppers damaged vs good ones you harvested seems mostly normal.

Some varieties/types are more prone than others...genetics, etc...

Yeah, I see that in rare cases. I eat them anyway.