I think you and your husband are both right. I think what you need to do is put her back in the xpen for a couple of days, and then WHEN she goes out, make sure to you have the time to watch her carefully and as soon as she starts to go pee, Say NO, or use squirt her with water, and then herd her back to her litterbox, or put her right in front of her litterbox and get her to jump in (while saying the word litterbox) Do this everytime. If she continues, then put her back in the xpen for an hour or so. This is a real pain, and in a way it is a battle of the wills, and who has time to watch their bunny every second, but in the beginning, if you have a stubborn bunny, it’s what you have to go through. But you have to claim the general territory as yours. You may even have to gradually allow more freedom by blocking off access to areas of the home with an xpen.
Good luck and keep us updated. OH, and be sure to put something great in her litterbox when she returns to it – does she like mint or rosemary, and or cut up a raisin into a few pieces, or a few carrot shreds within the hay, so that she sees her box as a great place to return to, not punishment.