1. There was a bug with a previous version of the addon where it would only include the pets shown in your journal -- so if you had anything filtered at the time you activated the addon, any filtered-out pets wouldn't be imported (even if they were collected). This has been fixed in the latest version of the addon available here
2. Make sure your current Armory count isn't counting any duplicates.
3. Try running the addon again -- we did just add a few more pets to the site that you may have collected in-game but they wouldn't register here if they were missing from our site.
Beyond those explanations, I'm not sure. *shrug*