1. my rabbits are housed in hygienic wire bottomed cages.
2. whenever I've had to litter train a rabbit it has been so unbelievably easy to not even be an issue.
When I've advised people on litter box training I tell them NOT to put the litter box in right away, but give bunny a chance to pick their potty corner (with young bunnies can take a week or so) THEN take the dirty litter, place in litter box, put litter box in the same corner. Hanging hay in the corner seems to help.
With adult bunnies I just take some urine based litter put in a litter box whereever I like and the adult bunny will use it without fail.
BUT recently I had a lady email. She's having trouble getting a 100% litter box trained bunny.
Well.. I've been talking with folks. Getting a 100% trained bunny is not generally going to happen. You see what happens is that rabbits scent mark. They will almost always leave some bunny berries behind as they explore their living space.
Bunny berries are REALLY easy to clean up. Just sweep 'em into a dust pan and into your composter if you have one, or garbage if you don't.
NOW the problem may be that your young rabbit is maturing
Maturing rabbits, just like maturing teenagers, sometimes have less than ideal bathroom habits. They have to deal with hormones and learning (or re-learning) correct habits. Give them time to sort it through OR if it's being problematic... Get a neutering job done. Neutering helps get rid of the hormones (particularly in a boy rabbit) and will in a girl rabbit as long as the job is done completely.