That being said, here are some reasons that your bun may not be cooperating.
This may be one of the easier things to fix. Rabbits can feel very nervous in new surroundings. If you have recently moved her litter box, or even more impactful, moved houses, this can mean lots of extra stress. She will take some time to get back into the swing of things. The introduction of a new pet can also be very traumatic. Rabbits do not like change.
HORMONES AND INSTINCT
If you are working on how to litter train a male rabbit, especially one who has not been neutered, overcoming his urge to mark his territory is going to be an uphill and lost battle. We highly recommend that unless you are breeding your rabbits with careful thought and good reason, that you spay and neuter your buns. They are going to be happier, and so will you.
Often times over zealous and or anxious rabbit owners decide to start training their rabbits too young. If your rabbit is under 6 months you might want to play the waiting game. She will grow wiser in a couple of months. Just be patient. Oh, and since she is still young get her fixed. (4 to 6 months is the ideal age to do so).
CHANGE IN MATERIALS
Some buns are super picky about their bathroom locations and surroundings. If they were using their litter box perfectly and now they are not, consider what might have changed. A change in the type of litter, box, cleaning solutions, hay, and location can all play a role in accidents. Think back to the times when you had the most luck with your rabbit using their box and go from there. Small adjustments can set you up for maximum success. Be careful to not over-think this though. There is a secret recipe and it is usually simplicity.
It is not uncommon that litter boxes that are too large or too small play a role in accidents. Watch your rabbit using their box. If they are having a hard time turning around, digging, or are generally hanging out of the litter box then it’s probably time to spring for a little bigger box for them. If you invested in the extra spacious model, then you may need to downgrade.
Incorrect litter can be a contributor as well. Make sure that your litter is safe for your bunny and is as neutral as possible. The smell might be appealing to you, but it may be overwhelming to your rabbit’s highly sensitive nose.
LOCATION, LOCATION, LOCATION
Does your rabbit always poop in the same spot outside of his litter box? Slowly moving the litter box in that direction, and putting all of the stray poop into the litter box might be the easiest solution for this one. Sometimes when rabbits are given too much room to roam they find spots to go to the bathroom in each area they're allowed to roam in. Limiting their space is possibly your best option, or investing in multiple litter box setups.
Rabbits like to dig, especially when they go to the bathroom. This has the tendency to fling poop out of the box and onto your floor, which is not where you want it. This is going to be one of those nearly impossible things to change. Sorry.
Your rabbit may be getting poop stuck somewhere on her fur, and then when she jumps out it falls off, onto your floor or furniture. This might be correctable through improvement in diet. A rabbit’s poop should not be sticky. If it is, she probably isn’t getting enough fiber, which is found best in quality Timothy Hay.
Sometimes my rabbit won't poop in the litter box. But it's best to rememeber your rabbit is an animal, and even if all of these items can be meticulously addressed 100% success is near impossible. Make sure that there isn’t and easy fix, and then chalk up the rest to the issues that come with owning and caring for your rabbit. Taking the time learn how to litter train a rabbit is worth it overall, but it is not a perfect process, and sometime the causes of accidents will remain a mystery. Good luck!