Looks like catfacing. Links to pictures of catfacing below.

This is a natural occurrence. Some varieties are more prone to catfacing than others, but this should lessen or go away entirely on later fruits. It's a deformity, but not a disease, and can happen when pollination occurs at low temps (i.e. below 50F).

Sometimes catfacing runs through the tomato and ruins the fruit; other times it's just ugly but doesn't have any effect on the edibility of the tomato if you cut away damaged areas.

It's your call as to whether or not you want to let the tomato reach maturity and see if you can cut away the bad spots. If the hole is deep it may invite pests but, other than that, most catfaced tomatoes are salvageable and edible. They're just not very pretty. :-)

Here is a link that might be useful: Some of these tomatoes have catfacing.