I think my rabbit hates my cat

[NotaCocoaPuff]

Does anyone have experience with a rabbit that might not like its feline house mate?

For months now I have been trying to figure out why my one rabbits keeps marking near the cats litter box. I've tried EVERYTHING to no avail. I even ripped up a rectangle of my pee-saturated carpet to see if it would help by removing the smell. It did to a degree. I them added another cat door so that the cats littlebox is not outside away from the bunnies (who roam free on the patio). It helps for a while but now my smart little Basil has figured out that she can get through the cat door into the cats litterbox. She poops and pees all over it. She also pee's just outside the cat door (which is directly next to one of her litterboxes). She has also nipped my kitty several times, luckily with no injury.
Basil's sister seems to have no issue with the cat and the cat has no issue with the bunnies.
Does anyone have any insight on how to help these two get along or how to stop the marking?! I thought this was a litterbox training issue but I strongly believe this has something to do with Basil and the cat.

 

[JBun]

Oh it's definitely territorial marking. Basil obviously thinks she is the boss and is making sure your kitty knows it. She is trying to establish her place as boss in the animal hierarchy in your house, and the nipping is to let your kitty know this and put her in her place.

They almost need a way for that hierarchy to get worked out, like is done when bonding rabbits together and done safely, but not sure how you could even do that with a cat and rabbit since they have different body language.