Noticed this(small) bug yesterday.
I marked the Guardian Cub as "not collecting" (Cause I actually did not want any pets bought for Money).
Then I had a change of heart and bought the cub on the AH.
After that I importet my pet collection from the armory.
Now the cub shows up in both lists. "Collected" and "Excluded". In the menu for exclusion/collected/not collected it is correctly marked as collected.