Well, some rabbits have a hard time understanding that they can not go where they want, once they know they can go there at times. That pen is pretty small, pretty much just a lookout to see where he wants to go, no place for things to occupy him, like cardboard boxes or tree branches. The times you let him out don't seem to match the times when he has the urge to be active.
I would consider using that pen to block the door of the room, and bunnyproof the room, like covering the cables, or protecting them with those plasic spiral protectors. It helps a lot if the cables are not hanging free, but are secured to a wall, desk leg, or corner. Or making a bigger pen where you can arrange things so he doesn't get bored, but with a small room it might be easier to just let him have all of it.
I covered pretty much of my house in rag carpets and cardboard now, works fine.