I am having exactly this problem, too. My seven-month-old male Lionhead, Benjamin, is well littered-trained -- really, he trained himself -- but all of a sudden he has been leaving a lot of pellets and urine marks on the bed when I give him the run of the apartment. I am washing the bedding as soon as he marks it, but it does not seem to make a difference. One day when I tried to shoo him off the bed, he even sprayed me! But he is not leaving any urine marks, and very few pellets, on the hardware floor; he's just using the bed as a litter pan. He has a regular litter pan in his pen, and another out on the floor, and he uses both of those.
I assume he is marking the bed in part because it is my bed. Benjamin is very sweet and physically affectionate toward me.
He is such a well-behaved bunny otherwise, but this behavior is driving me a little crazy. Might he outgrow this? He is a cryptorchid (undescended testicles), and my vet was not enthusiastic to do risky exploratory surgery in his abdomen to try to find what might be very tiny, unformed testes. Therefore, I may always have an unneutered cryptorchid male.
He loves time out of his pen, so I guess that I will have to block off the bed (as discussed) or cover it with plastic. I do not want to keep him penned up all the time. I do hope that in his case, this turns out to be an adolescent phase, although I know that for some males it is a more permanent state of affairs.
Any additional advice?