Will she take a treat from you? Has she been eating and pooping? Those are the most important things when trying to figure out if your bun is sick.

Some pets are very subdued and sweet when you first bring them home, then as they settle they become more lively and might show fear and aggression. Baby bunnies also do tend to run around like crazy. Puppy dogs do that too, it can look scary because they seem kind of out of it.

Bonnies don’t like hay in the litter box, I did it once for my bunny and ugh never again, if I have to use hay (Most of the time its hay cookies) I place it near his food bowl away from the litter box, litter box is for number 1’s and 2’s, if you use it in the tray, 1, its a mess to clean as hay does not absorb number 1’s, and 2, Bunny may go off his hay thinking its for his Bunny business (Like mine did once not the one I have now but another one) because they are clean animals, (Even though they do eat their own poop.) I’m sure it can be used in an emergency like you need to get some litter and can’t go to the shop for an hour or so for litter, hay racks are good, we use hay cookies so no need for a rack.

For the hay question, My bun is very different from Pinkys, I think all buns like there stuff certain way. For example, I have her litter in her litter box and on top of the grate that she stands on i put timothy hay, which she uses the bathroom there. My bun does not like to eat timothy hay, she nibbles every now and then, but she knows thats where to use the bathroom 1’s and 2’s. My bun (still only a couple months old) eats alfalfa hay and orchard. She loves those and she eat’s timothy based pellets. She knows if there is timothy hay somewhere thats where she uses the bathroom.

You should put hay someplace outside the litter-box as well as in it, because you want her to always have fresh hay. Some buns like to have a nibble at the same time as they go to the bathroom, some buns don’t. But there’s always the risk of litterbox hay getting peed on, so you should offer some in another place as well. There are little wire-balls you can stuff with hay and hang up in the cage or you can have a hay-rack so she can pull hay into her cage through the bars. That way the hay won’t get dirty.

There is no one right way. Bunnies are different. Mine poop and pee on hay, but in the center of their litter box. They eat the clean hay around the edges. With these two – the hay rack has to be the type where they pluck hay out of a vertically hanging rack that they can’t sit in. If they can sit in their hay rack, they will poop in it. Same with their food bowl.
My other pair – poop/pee on the side of the box that is right in front of their food bowl. They don’t ever go on the other side of the box. So one half is pooped/peed on, and the other half of the hay is eaten. When I change the box (every day), half of it has hay on the grate, the other half – the hay is completely eaten from the grate. Those two have a hay rack, but they don’t use it. They prefer to eat from the clean half of the litter box. (The box is 18 inches wide, 28 inches long).

Bunnies are den creatures. They like to spend time in their hidey holes. Mine like to spend time in cardboard boxes. My first two that I described, like to lie in their litter boxes too.

Yes, they really are den creatures =) My Yohio spends most of his day in one of his 4 cardboard box-houses. When I approach, he sticks out his little head thto see if I have a treat or two for him.

Freedom of choice is great – if a bun can choose where to be, it can move to a different place if it wants to and it knows it can move if it wants to. Both my buns have 2 litterboxes each. They use all of them.

My pair that are super duper good about only pooping/peeing in front of the food bowl on one half of the litterbox – they only have 1 litterbox. The other pair have 3 boxes. Guin And Lancelot both use the main large box (18×28). He has a smaller puppy training box that I gave him to use when Guin was beign bossy and kicking him out of the main box. I haven’t seen her use his puppy box. He has one of those smaller “jumbo” rabbit litter boxes, triangle in shape, really small in my opinion. It’s in the back bedroom. I made a small access flap in the screen door, so Lancelot can come out and have free roam of the back half of the house. It is too small for the cat to use (there are birds loose in the rabbit room), and Guin has always refused to come out. So Lancelot occasionally uses the box in the back bedroom. He doesn’t have a box in my bedroom. I gave him a box in that room because one day after cleaning house, I forgot to leave him a towel/rug to step out of the room and find his way back to his room. My bunnies won’t walk on the bare wood. So since there was no fabric walkway for him, he chose a corner, and this is really impressive – he dragged over the plastic vent cover, flipped it over, and used it to poop and pee in. When I got home from work, I realized what had happened, replaced his fabric walkway, and gave him a litterbox in that corner.

Your original concern was on twitching and running around aimlessly -was it like this?

https://www.youtube.com/watch?v=yh2XsLGPbNg

https://www.youtube.com/watch?v=dSP5BsHt7nw

What lovely binkies. Reminds me of the kits my bunnies had. They sure did seem to twitch and run around aimlessly. Terribly cute.