Currently we can't use things like breed changers or marking items on pups which is a bit frustrating on its own but it's not exactly the end of the world. You can get through it by waiting until they grow and then using the items.
However this knowledge did make me think about the fact that it makes it impossible to alter any perma pups. In order to apply any changes to them, you'd have to pay for the item to turn them back to an adult and apply them. And then if you want them to go back to a perma pup, you'd have to buy the perma item again. And both of these items are premium currency.
I figure this is likely an oversight but it still needs to be fixed.