Problems house training

Two months ago I bought a house rabbit. She loves to hop around my double bed, and for the first month and a half of having her, she wouldn't mess on it at all, however I can't have her up there now because she is guaranteed to wee and I have to have the whole duvet cleaned. She has a litter tray in her cage which she is trained to use, but I can't seem to convince her to use the litter tray outside of her cage as well and wonder if this is related to the bed messing incidents.