Is the crate simply too big for her, so she feels there's room in there for "her" space and also a potty space? I know she's teeny, maybe after you completely clean the space (use special stuff you can get at any pet supply place - Nature's Miracle, or something like that) so that she cannot smell it any more, move the crate sides in if its adjustable, or just block half the space off. You don't need to give her a whole bath, but can just clean off her backside w soap and water ...