Most times when cats do this they are insecure, afraid, or are hiding in their litter box. It smells like them and if it’s one with the cover, it makes them feel safe. If things have changed in your home–if you have moved, have a new dog, cat, more people, have the litter box in a high traffic area–these are things you need to consider, then put the box somewhere where the kitten feels secure.
Make sure she has her own bed with her blankets, also away from things that scare her and where she feels safe. A cat tree where she can climb up and get off the floor and able to look out windows.
Hope this helps. Cats aren’t grossed out by their pee or poop, but usually it’s instinctual for them to bury it since in the wild their poop would lead predators to them. Sounds like she is having issues with something that is making her feel insecure. Keep us posted!
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