Most likely it is a fungal disease called Anthracnose. It is hard to control because the spores splash up when the tomatoes are small and green. The spores do not grow until the fruit starts to ripen. The symptoms start as small sunken circular spots that can expand as the fruit ripens.
Since the spores are on the fruit before you see the damage, a fungicide would not stop the spread of the disease. If you are going to treat ask your county extension service for a recommendation. You will have to treat the plants as the fruit is set.
Tips to avoid Anthracnose
- Make sure your soil is well drained
- Keeping plants staked or cage to prevent them from resting on the ground.
- Rotate you crops
- Avoid getting the plant wet when you water
- A mulch like straw can help prevent the spores from splashing up
- Remove all garden debris at the end of the season
