Since I'm sure I am not the only person here still suffering from this bug I decided to go ahead and make a thread in the official Blizz bug report forum. I was hoping that I could count on my fellow pet collectors to help me compile a list of the pets that are not being added to the total count.
I have a theory that the bug applies to pets that are not showing when using the "sort by current zone" option via the pet journal enhanced add on. They dont show because the zones are not spelled correctly in the journal. I'm not 100% on this theory but, I dont know, I thought it would be a place to start.
So please let me know what pets you've found dont get added to the count and if you could post in the thread on the Blizz forums too, that would give the developers an idea of how many people are concerned about this issue. (http://us.battle.net/wow/en/forum/topic/7273267737#1)