you normally see mottling on the leaves with virus. I don't think this is what is on the fruits. The nobbly skins are common and normal and I assume you mean the yellowing parts. Cut one in the area and see what it is like under the skin. I suspect all will be well.

It looks like the work of thrips, or some kind of skin miner, to me.

They say that beauty is only skin deep....well, so is ugly. In any case they look very edible.

I wondered it it was snail damage.