Welcome : )

Some bunnies aren’t chewers so no need to worry. It will probably be a blessing in the long run. Does she eat a good amount of her hay? The hay is adequete at keeping the teeth trim.
You could try fixing her chew toys down in her cage. She might have a go at them more if they don’t move about so much. It becomes more of a project then.

When she pees outside the box, is it nearby or other side of crate?
What size litter box does she have?
You could try a less absorbant surface to line the crate. Some just continually pee on absorbant things.
Also, at 3 months old you might see her habits go awry due to her hormones arriving. Bunny puberty!

My apologies. I edited my post before as I initially hadn’t read your edit describing the set up. You were probably replying at the same time.

It’s hard to tell how big the box is but typically those corner style boxes end up being too small for growing bunnies. Though the high back is great, the front can be too low if they pee facing the back. They’d pee over the low side.

Does she toilet near the other bowl of hay you have for her?

Try a large rectangular litter box with deep sides. (I’m not certain what dimensions to suggest as im not used to thinking in inches :p ).
Then you could put all the hay in there. That should help keep it contained.

By all means post pictures! We love to see the bunnies.

I’m not sure if this might help.  But what I do is cut a cereal box in half. And I have done two different things with it. I had cut two holes into the box and bungie corded it to the side of the cage right in front of her box. Skipper kept break the box because she would paw at it to get the hay out of it. So tried something else that seemed to work. I had cut the cereal box in half and bungie corded it to the litter aroundt he sides. It worked out well except that the cardboard didn’t hold up too well. I’m trying to find a way to make another version of it with sturdier sides.

I would definitely take the carpet out of the crate for now – some bunnies can’t resist peeing on absorbent surfaces. I would also find some way to put the hay up above the litter box so she can only eat while she’s in there. I know mine think anywhere there is hay is an acceptable place to pee, so confining the hay to one specific area makes them go only in the their litter boxes.