Pet food is deliberately rather rare and no changes have been made to the frequency that it appears in the Magic Academy. The developers want players to have to choose which pets they use it on. They also do not want to make it too easy for cities with multiples of the more favorite Pets.
To increase your chances of Pet Food appearing make sure you're checking the Magic Academy regularly and have nothing cooking in the Relics recipe slot at the reset, as that is where Pet Food appears. You can also use Sips of Clarity to change the recipes for additional chances at getting what you'd like.
There will be some additional options for small amounts of Pet Food in the Future, but you will always have to be selective about which Pets you use it on, Pet Food will never be one of the items that will be easy to hoard.