Limited Pets means that there are some pets that are not readily available through the normal adoption link. There are currently 9 limited pet species. They are:
Some pets can be obtained by items, such as the Aeanoid which requires an Aeanoid Seed to be planted. The Darkonite and Swampie are not so much "limited" as they are 'mistakes' from the Pet Zapper, the Swampie being the most common zap.
The Bumbus can only be obtained by doing a quest for the Bumbus Queen and the Neela is available for purchase from the Cash Shop. The Bhakoru can only be gotten by those who completed the Blake Steele Plot and visit the Crystal Room.