We have a rabbit.
They are good pets.
The thing is, sometimes stray rabbit pellets/poop just sort of drop at other places by accident.
But, if the poop is piled up somewhere else (like intentionally), besides in the litter box, then the rabbit has made another spot, a place to poop.
The rabbit does know where to go, IN the litter box. But well, sometimes pellets just comes out.
I actually watched our rabbit to see what was going on... she'd be IN the litter box, peeing/pooping... then hop out... but then, there'd be like some other 'stray' pellets still sort of dropping from her butt, even after she hopped out of her litter box. Ahem... sorry for the detail. LOL
Our rabbit is perfectly healthy and litter box trained and spayed. But from my observations, this is what was happening and I saw it.
Or, you put 2 litter boxes around... if it is a large room. Like a basement.
Also, put things out, for her to play with and knaw on.... rabbits, NEED to knaw on things and you don't want her to knaw on your home or electrical cords.
We have our rabbit, loose, and out on an enclosed balcony. We have 2 places for her to poop/pee.
all the best,
Susan