If 100% litter box adherence isn’t “clicking”, you need to do some active litter box training. The way rabbits mark and are active makes litter box training pretty intuitive for them, but this doesn’t mean every rabbit will understand it on their own. At the end of the day, we’re telling rabbits to go to the bathroom in this weird box for, what’s to them is a reason beyond their comprehension (i.e. it’s more clean for the owners and is easier for us to manage). I recommend spending some time with her and the litter box, and any time she’s about to pee or pees outside the litterbox, you put her in the litterbox so the connection is made.
It could also be the hormone spike following the spay, which makes it difficult to be 100% adherent as well. This will fade away naturally, but doing some training to reinforce it wouldn’t hurt.
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.