Yes, the Carefresh is confusing them. Part of it is their age and the fact they are not neutered yet, but the best thing you can do right now is to remove ALL bedding from the bottom of the cage. No Carefresh, no litter, no hay, no blankets/towels, no pet beds. Only have litter and hay IN the litterbox.
I’ve used this analogy before… Imagine being in a room with a dozen toilets, but you’re only allowed to “use” one. And no one has told you WHICH ONE! This is what you’re doing to the bunnies… you’re giving them a dozen toilets and then getting frustrated when they don’t choose the “right” one!
They are still going to pee on the cage bottom from time to time. Newly weaned bunnies are basically like a 2-year-old toddler who is just starting to learn potty habits. There will be accidents. Just clean it up and drop the wet napkin/paper towel in the litterbox. They’ll catch on eventually.
Also, make sure to limit out of cage time right now. They’re not ready for an 8 hour free roam session. Have them out for 30 minutes or so and return them to the cage for a bit. They need to start associating their cage (and then the litterbox) with where they’re supposed to go.