Not sure what's going on...

[Swtairen]

I'm trying to figure out if I did something strange or if I need to do a pet by pet comparison...

My achievement and this site show me as having 501 pets but my window only shows 499. Am I missing two pets that I had before and released somehow or am I trying to see pets that I have on an alt but can't see on my main?

[Quintessence]

or am I trying to see pets that I have on an alt but can't see on my main?

This. The culprits are the Guild Page and Guild Herald. These pets only appear in the Pet Journal for the character that purchased and learned them. Plus Alliance can only view the Alliance version, while Horde can only see the Horde ones.

Your WarcraftPets collection, however, shows both versions. So 501 total (includes both Alliance and Horde versions) minus the two from whichever faction you're not viewing your Pet Journal on, equals 499.

Hope that solves the mystery!

[Dakaf]

The only time it really matters is when you're one away from an achievement. You look here and it shows like 400 or whatever. Go in game and you have 399. Other than those specific instances, it's pretty irrelevant other than to brag. Just point them here and they'll see how awesome you truly are!