I see that once in a while and it really is yucky when you reach out and grab one that is rotting like that. It seems to me it is similar or the same as what sometimes happens with tomatoes that is called sour rot.
Brown spots could be stink bug stings or leaf footed bug stings. That is a major problem at times here. I had to spray all my peppers a week ago because of stink bug and leaf footed bugs starting to multiply and mess up too many of the fruits. I have never associated those stings with the water filled stinking bell peppers but maybe that is how the bacteria gets started in some fruits.
Bill