You putting bedding in there will only help confuse his litter habits, do away with bedding entirely from his cage, just in his litter boxes. My rabbits would go all over the place too if I put carefresh down. I have two fleece blankets down in their room they can use as a bed if they like and that is it. You don’t want to use towels since if they chew the threads can cause a blockage, fleece comes apart differently and has less risk if they nibble a bit.

Exactly. He doesn’t need bedding, and the litter only in the litter pan will help him know that it’s the place to pee. Soak up his pee outside the pan with paper towel and drop it in there, so it smells like his pee, too. Make sure his litter pan is big enough for him now.

He may be mad about something. Sometimes they make a big mess because they are stuck inside when they want to be let out, or are hungry for a snack, or they don’t like a change in litter or food, or it’s Thursday. Fickle, unpredictable, and usually a mess is their way of telling you something, but it’s hard to figure out exactly what.

You can use fleece to cover the floor, although and even thinner (ie less edible) is 100% cotton flannel. I sometimes just spread out a sheet, or buy a yard of it from a store like Walmart where it is super cheap. It’s smooth to lie on, but isn’t anything like litter and isn’t too warm in the summer months. Some bunnies actually prefer lying on tile, wood, marble or plastic flooring just to be cool on a smooth surface. So rid him of the bedding and see if his behavior improves.

Can I ask how big his cage is? Store bought cages are too small for bunnies, and I know Riley is a larger bunny. He could’ve been angry that he’s in there, or it could be that he simply doesn’t have enough room? When Lady’s pen was smaller, she’d try to jump out, but besides that she’d end up peeing in her food bowl accidentally or jumping in her water.