I've noticed lately that the way pet duplicates are listed seems to not quite work right, in that it only counts duplicates for the current shown listing, not the collection as a whole.
An example, to clarify what I mean: My collection currently holds three Curious Wolvar Pups (gotten back in the first year since I did that quest on 3+ alts, yet was silly enough not to pick the oracle for any of them. Ah well, just a couple more weeks 'til Children's Week... I digress).
Having found a few humanoid battle stones, I have upgraded one of them to Rare quality. So currently, my Wolvars are Rare 10, Uncommon 1, Uncommon 1.
If I show my collected pets, the two uncommons are appropriately shown with the orange overlay for being duplicates. So far so good.
However, if I filter my list to only show my uncommon pets (because I want to get myself a list of pets I still need to upgrade with battle stones), only one of the two will be listed as a duplicate - the first one will be considered a "primary" in the listing. This is of course a danger since it means that if I don't know this, I'll accidentally flag this pet as needing to be upgraded even though it is in fact a duplicate.
I suspect this behaviour might also be why excluding duplicates through filters isn't working. If you try, it still shows all the duplcates... at a guess, while the filters are still being applied, the system doesn't know yet what is a duplicate or not (or doesn't check it properly, rather).
EDIT: Added screenshots for clarity. =)