Hi. Yes - they should have been included! I feel so sad for your family, and kids. How totally frustrating.
This happened to me once - we traveled to a wedding - I was a bridesmaid & my husband was a groomsmen. The photographer didn't take a single photo of the wedding party, or our family. My feelings were hurts for months. I finally decided that it was the photographer, not the bride, that had made these decisions. The photographer was so involved in the bride & groom, he forgot about everyone else. Perhaps he was inexperienced.
Since then, whenever I have helped with weddings, I make sure that one person is in charge of working with the photographer, with a well defined list, and plan of action.
Here is a list of wedding photos to consider for every wedding. As you can see, flowergirl & ring bearer are mentioned several times.
http://www.myplanninglists.com/wedding-photos.php
At this point, I would probably let it go. The bride was distracted that day. But you could make sure that any wedding you help with in the future has all the appropriate photos included.
Also - in the future, I would bring a camera - and take the pictures you want for your own scrapbook.