We do not recommend that people can tomatoes that have spoilage issues.  It could result in spoilage of the final product due to changes in pH (acid levels)  in the remaining portions of the tomatoes.  This includes sauces and salsas with other ingredients.

However, you could make the desired products and safely freeze them, since there are not safety concerns with acid levels in frozen foods, like there are in canned foods.

Be sure to cut away any spoiled portions of the tomatoes before use and cook the products well.  Check the instructions on the sprays you used to make sure they were followed correctly so no possible toxins from the sprays remain in or on the tomatoes.