Being unspayed, her territorial instincts can pop in at seemingly-spontaneous times. My thought is she was feeling uncomfortable in exploring at the beginning, so using her litter box was based on her comfort zone. Being with you longer now, she’s grown more comfortable and exploratory in venturing to mark her territory and expand it. Marking their first cage is extremely common and I don’t know of an owner who didn’t run into that within the first week of ownership. Some dissipated this habit right away, while others have it lingering until they are fixed.

I would suggest continuing litter box training, so moving the poops, moving her, etc.. It’s helpful to designate a sound which will signal to her “Hey, don’t do that.” It also helps to have a sound you can readily make because sometimes you can’t run across the room immediately to prevent a pee or signal that poop was ‘wrong’, but you can at least make the sound immediately so it registers as “That sound happened just when I pooped there. Now the hoomin is taking me to the box.” For Wick, it’s a terse hiss, as rabbits inherently hate that sound (i.e. sounds like a snake).