If they are on the outside of the apple then they are likely to be Scab. If they are inside on the flesh of the apple then it is probably Bitter Pit.
The former is dealt with by spraying every couple of weeks from when the fruit first forms to a fortnight before you begin picking. The spray is Copper Sulphate or Bordeaux mixture, both reasonably organic.
If it is Bitter pit then there is not much one can do. This is caused by a Calcium deficiency and it is hard to get Calcium into the tree. It is more prevalent in wet seasons and on acididc soils. You can try what we have done this year and drill holes down into the soil round the trees and fill them up with lime. The apples are not ready yet so no idea if it has worked.