Birds will sometimes take a few pecks and can make clean shaped holes, i know they do it with peppers. The dusky sap beetle can make a clean shaped hole, but smaller than the one you described. There's a good chance that i'm wrong, in your case, so take my guesses with a grain of salt.

Also: many here would want to see a pic before hazarding a guess.

Another possibility is tomato fruitworms. I control those with a BT liquid spray applied once a week, it is an organic pesticide that only kills caterpillars.

My first year growing tomatoes, caterpillars ate all the tomatoes that I got (it was a bad harvest anyway due to extreme heat) so I've used that ever since.