I know a lot of threads here are about litter box habits, so sorry for the repeat, I’ve just scrubbed up two pee spots and swept up a bunch of poos. I have had Totoro since I adopted him in October. His litter box habits have not been good this entire time. In the beginning he was confined to an xpen for the night and is habits were okayish. He was bonded with Wilbur in November and they live in my room together without a cage. At first it wasn’t that bad, but over the past weeks he his habits have regressed. He started poop all on the carpet and I started finding aboout 6-8 spots of full on pee spots on the carpet a day. Wilbur started pooping outside of the box too, but she makes about 80% of the time in the box. She used to be 100% trained. I have confined them to an xpen that isn’t connected with itself, both sides are attatched to a wall. There are 3 litter boxes in there. They use the litter boxes but Totoro still poops and pees everywhere and I find a couple Wilbur poops outside the box too (hers are much much smaller). I started clicker training Totoro yesterday. Should I make their space smaller? What should I do about exercise time? What more should I be doing? 

I feel cruel confining them, they aren’t used to it but they must be trained. It was driving me nuts to always be accidently stepping on rabbit poop everywhere I went and constantly trying to get urine out of the carpet. 

Edit: For the clicker training he has already started to associate the click with a treat (I’ve been using pellets). Everytime I see him in the litter box I give a click and a treat at the same time. If I see him lift his tail, I lift him up and put him in the box. I can’t watch him all the time to be more consistent but this Friday my winter break starts and I will have 2 full weeks to devote to the bunnies and clicker training.