The holes may be the result of caterpillars. Some caterpillars are little trouble and we tolerate others because they are the larvae of butterflies and moths. When they are eating desirable plants as this one is, suggest you physically remove all you can see or spray with an organic control such as Bt (Bacillus thuringiensis is a contact spray only), or another organic control formulated with Spinosad (has a 7-10 day residual) available at your local garden center. If spraying with Spinosad, do so in the early evening after the bees have returned to their hives. Once the spray has dried it is safe for beneficials. Before you do this, however, cut open the damaged tomato to see if there is a larva/caterpillar inside. If not, then the damage may be due to birds or rats.
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