One idea is by the end of the day, the litter box is too “soiled” that he doesn’t want to use it anymore. I give Wick’s litter boxes at least 2 cleans a day to prevent that, because he does not like using a soiled box.
Another idea is these are the result of his bottom being over the lip of the litter box and not landing inside. This is under the assumption the litter box is low-lipped. The solution to this is getting a high-walled litter box, or attaching panels on the litter box so Peter needs to jump inside in order to use it. Wick’s litterboxes are all high-walled so the occasional poo may fly out when he’s jumping out, but that’s it.
Lastly, an additional thought is, if Peter is not neutered, he is trying to mark his territory there further using marking poos. This can be lessened by doing more litter box training, but will not completely dissipate in most male rabbits until they are neutered.
See images at http://www.instagram.com/wick_theboogeyman for a peek at what Wick’s litter boxes look like.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.