Before anything else, are you certain that this fennekin always acts like this, even when in the company of its proper trainer? Sometimes, stress can cause pokémon to revert to behaviors associated with younger, untrained pokémon, and the kinds of behaviors you’re describing can also (rarely) occur in pokémon that have been traded. This is because they’re under the impression that they’ve been abandoned by their former trainers, so the first step is actually to reassure them that they haven’t been abandoned at all. It’s just that in your case, whereas traded pokémon need to be reassured that their new trainers love them, you have to convince this fennekin that its old (or, well, current) trainer loves it. This is why she hasn’t recalled fennekin and deposited it in the storage system for the few weeks she’s gone, after all.
So although it’s a bit too late to ask if your friend has a routine with fennekin, it’s worth it to establish one now. Give this fennekin the same amount of attention, affection, and training you give your other pokémon. Use this fennekin in battle to help establish a bond and a level of mutual respect. Do everything you can to treat this fennekin as one of your own pokémon, and it will begin to acclimate to your home.
If this is just typical behavior for your friend’s fennekin or if you need to give her guidance on behavior in yoru home, meanwhile, use positive reinforcement and begin with the simplest thing to correct: housebreaking. Lay down newspaper and whenever you see this fennekin relieving itself anywhere but the newspaper, pick it up and put it on the patch you’ve covered. Any time it relieves itself on the newspaper, reward it with a treat. Eventually, it will begin to associate relieving itself where you tell it to with a reward, which in turn will make the rest of its retraining far, far easier. Use the same tactics for each of the other behaviors. When you see fennekin clawing your furniture, push it off and give it a toy. If it plays with its toys instead, give it a treat for doing so. Place your pokémon’s food bowls far away from this fennekin’s, and any time you see it eating from your pokémon’s dishes, pick it up and carry it to its bowl. If it eats from its bowl (and only its bowl), give it a toy. Reinforce these lessons with words. A simple “no, Fennekin” in response to bad behavior and “good Fennekin” in response to good behavior is enough.
Of course, all of these lessons may be moot if your friend doesn’t actually train her pokémon, but at the very least, this fennekin will understand proper behavior in other people’s homes by the end of this training session.
As for what you should tell your friend, because of the first paragraph in this response (and the uncertainty of whether or not this is normal for her fennekin), it’s extremely unwise to accuse your friend of failing to train her fennekin. However, it’s also vital to be open with your friend, in case this is indeed an issue of either bad training or separation anxiety. Tell your friend that you’ve noticed some strange behavior in her fennekin at first and describe the behaviors you’ve encountered. Also tell her what you’ve done to help her fennekin adjust to your home but never accuse her of being the source of her fennekin’s problems. If you phrase it politely enough, you may be able to convince your friend to look into either her fennekin’s mental health state or reinforcing what you’ve taught it.
In short, yes, it’s perfectly fine (for the sake of both your sanity and your home) to train your friend’s fennekin. It may even be vital to its mental health. It’s just that when it comes time to give it back, be as gentle as possible to both the trainer and the pokémon.