Where the spots are on the fruit it is rotted on the inside. Even the healthy looking red fruit tastes bad.
What Are the Black Spots on My Pomegranate Fruit?
Pomegranate is generally disease and pest free, but there are a few pathogens that can infect, and it sounds like you have a fungal or bacterial infection. You might be able to find out the specific infectious agent if you take fruit to the county extension service; they can also tell you what would be best to use against it. This link will help you locate the closest one: