When my buns did that the vet said a "Little" paper wouldn't hurt them. I guess I'd be concerned if you are noticing a difference in the amount of litter you put in. On thing I did that works very well is I went back to the pet store and bought my buns a litter box that has a grided
tray that sits inside the litter pan (on top of the litter)....the inner tray allows poop pellets to fall through to the litter.
Then I put some timothy hay in it since they like to sit in the litter boxes and relax (and eat) plus it protects their little feet. It wasn't expensive and I really think it works so well that I bought 3 more of them.