I think this is working as intended because what would you expect the behaviour to be otherwise? Should the site tell her your pet limit is reached and force her to keep the pet? (Which btw would require it query about your pet count instead of just doing the transfer -- waste of resources and time) Should the site throw the pet into the pound instead? Burdening the user by placing hard limits usally detracts from a game. The limits in this game are soft limits the simply stop you from acquiring more while you're at/over the limit. They don't punish you for accidentally going over the limit -- which I feel like this is a really nice thing because otherwise I'd be stressing about my pet/item limit all the time and I would likely never try to get MORE pets/items from fear of punishment by the hard-limit. And then I'd likely quit this game because that's just not nice/fun/productive.
So really, we should just be glad this game uses soft-limits and respect the fact that while we can go over the limit on pets and items, we should try to be respectful and not do this, as much as possible.