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If you've made that same dish before, but this didn't happen, it was probably the variety of the pepper. All green bell peppers have a bitterness too them, which some people are more sensitive to, and simply will not eat green bells - only the ripe ones. Also, the slow cooking method does less to get rid of the bitterness than sautťing them, which is done in most recipes, before the rest of the cooking. If you find you are sensitive to that bitterness, no matter how you cook them, you may be one of those who will want to use only the ripe peppers.