There are quite a few pets that will continue to show up as uncommon, even if you upgrade them to rare in your Pet Journal. Hopefully Blizzard will correct this issue in the future.
Pets affected are generally those that cannot battle. These pets include but are not limited to (pets in bold indicate that they're in your collection):
Guild Page (horde and alliance)
Guild Herald (horde and alliance)
Your armory currently lists 47 uncommon pets, so add the 9 mentioned above and the result is 56 uncommon pets (as shown on your WarcraftPets profile page).
Keep in mind that your armory value and your WarcraftPets value do not match up because the armory doesn't track the quality of certain pets, but the quality of the pet item that teaches the companion.
Feel free to browse through Perks N Peeves
, my vanity pet collecting blog!