Do the holes go right through or are they part of the wrinkled skin of the tomatoes? If the fruit is intact its just the nature of them.

No the holes appear to go right inside before they close up. Not all of them do it.

I still think its the way they are - all puckered and odd. They won't taste any different. Having said that, could it be blossom end rot?

I also caught small slugs nibbling and then the wound heals over. rest of the fruit is fine to eat though.