I thinking you are doing everything right, an unspayed bunny in the midst of puberty more or less can’t be fully litter-trained. She has an urge (and it’s of course completely involuntary on her part) to mark her area as hers. So it’s not that she doesn’t understand that pee and poop should go in the litterbox, she sees alternative uses for her pee and poop, they are not just waste-products, they are important markers of territory. Once you get her spayed this should be much less of a problem. Until then – well, it sucks =(

I’ve actually read that about Carefresh before, we have had least one other member whose bunny didn’t tolerate it. You can use shredded newspaper, or you can use paper-pellets made of recycled newspaper (there’s a brand called Yesterdays News f ex) or you can use hardwood stove pellets. Hardwood stove pellets is the cheapest option. You don’t get it in pet shops but in feed stores and such, it’s not originally for pet use but for heating houses. I use hardwood stove pellets with my bunnies and it works very well for me, the used litter I recycle in my compost.

Moving to behavior.

Is the “bedding” just in the litter box?

So what’s on the floor then? I’m asking because having “bedding” on the floor can cause confusion, even if it’s a different texture.