Agree with Reeem. A few questions…
I assume they are bonded? If they are not – then they will mark until they have accepted each other’s presence.
How old are they? Young bunnies need to learn that they want to be litter trained. Young bunnies poop and pee everywhere. As they mature, they will be more inclined to want to use the litter box. I found that my youngsters started to show signs of improved litter habits by 6 months.
How big is the hutch? My buns all have impeccable litter box habits – except one female. If she is in a space that is smaller than 4×8 (as a single bun) and somewhat larger than that (with a second bun in the space), she will poop everywhere. Once I give her a larger space, she goes back to pooping only in her litter box.
Assuming your buns are not youngsters, and are newly bonded – how long have they been bonded? A newly bonded pair might still be pooping everywhere to establish rank.
How new is their hutch? They might still be “establishing” their presence in their new hutch.
Hope this helps.