My bedroom isn't bunny-proof, thus they are not allowed in there, ever. Once they got in, the baby gate wasn't latched all the way, but we noticed right away and let them smell around for a minute before shooing them out.
However. Amelia will sometimes pee in the corner of her pen. (The bunny pen takes up about 25% of the living room.) I also had to remove their old condo, as she would pee in the corners of it, and it had fixed carpeting for the flooring. I didn't even realized how bad it smelled until I took it out. (I did spot-clean with vinegar, but couldn't get it all.) I used to think she did it because she was lazy, and just didn't want to hop 10 feet over to the litter box.
Now she will sometimes pee in the back corner, but I think she might do it as a sign of disapproval. She hadn't done it in a long time, but then last weekend when our new sofa was delivered, she did it. (Thankfully after the delivery guys left!) She just looked out of the pen at us, hopped over to the corner and peed. When Jason went in to clean it up, she hopped over to him and bit the top of his foot.
I think she was just showing us that she didn't like all the hubub that was going on.
I will be making a new condo for them soon, with plywood shelves and World Market grass mats instead of carpet. I will also be getting a second (small) litter box to put in that side of the pen to try to encourage her to be a little more tidy.