It seems that the pet collection on the armory oftentimes takes into account the lowest level or worst quality if you have multiple of the same pet (but not always).
For example, if I have a favorited rare level 25 Spectral Spinner, it only shows the unfavorited uncommon level 23 version. Occasionally, some will show the level 25 rares when there are multiple, such as the Sinister Squashling (I have 1 level 25 and 2 level 1s and it shows the level 25). Winter’s Little Helper shows rare level 25 and favorited of multiple, but Rotten Little Helper only shows uncommon level 1 and not favorited (should also be a rare 25 and favorited).
It seems like an odd algorithm that is not working consistently. It’s been like this for some time, but my pet collection is much larger now and I can find more examples.
To add, I have logged into the characters recently so the collection is up to date. And pets added to the collection are almost immediately visible.