Community manager Nethaera hit the official forums this afternoon to notify players of a known display issue with pet collections. The notice reads as follows:
Known Pet License Issue
We are currently aware of an issue in which upon logging into the game, it may appear that some pets are missing. A fix has been applied to address this issue, though it may take a few hours before pets appear on the pet list again properly.
In other words, while your pet pane may display that you're missing some pets you've previously acquired, they haven't actually been lost. By the time you read this, the issue may even have been resolved already. In either case, don't panic: your pets will return soon.