The word that jumped out at me was “bedding”. It often can confuse the bunnies and delay good litter habits, because they don’t know the difference. You really don’t need bedding at all. Not sure what the bottom of your habitat is like, but a floor, low pile carpet or plastic is fine as a bottom without any bedding at all. You can use a little fleece for blankies to snuggle, but they actually have fur to snuggle with to sleep (each other) so even that isn’t really necessary. Seagrass mattes are good for their feet, make good flooring and is edible and good for their digestion so they are a win/win alternative to bedding.
That said, it makes it easier to determine what type of litter they like best. Some prefer pellets, like Yesterdays news, so that may be fine as is. If you think they would prefer shavings, try Aspen. NEVER use Pine or Cedar shavings, however. Carefresh is a soft alternative to shavings, and Feline Pine is a good alternative pellet litter, though my personal favorite is Aspen pellets with Aspen shavings on top. It’s a safe, odor absorbing wood that costs a wee bit more.
Take any pee or poo from their floor and put it back into the litter pan(s), They each have their own pan, right? Also, try hanging the hay from a hay basket above the litter pan, so they eat it while using the litter rather than using the hay AS litter. Bunnies like to be clean, and they would rather keep their food separate from the litter pan. (Except to eat cecals.) Hope these suggestions help.