A vet check would be the first thing to do.

And I think I would be looking for a way to contain the kitty for a while. Maybe a cage with a litter box. She would be reluctant to mess where she lives. Maybe you can borrow a large cage from a shelter if you can't buy one. Sometimes too much freedom isn't good for kittens. Once she learns to use her litter box in the cage, she'll be more likely to use it when she's allowed out.