Hi pandy, here's a helful site with various pictures of tomatoes with different problems. Most fungal or bacterial infections that produce mold or rot follow bugs feeding on the fruit such as stink bugs. The feeding leaves an open sore where bacteria and fungi can enter.

Let us know which you think it might be. Someone might be able to provide an answer to either avoiding or treating.

Pandy, Check out the fruit part of the TAMU Tomato Problem Solver linked below. Black on the sides of the fruit could be many things. In my garden when I see that, it often is anthracnose. If you post a photo here, someone might be able to identify it for you.

TAMU Tomato Problem Solver Ripe Fruit Disorder Page

Hope this helps,

Dawn