As PrincessDiana asked... How big is his crate/maybe there is too much room?
Also, if your free feeding him...you have to expect that he'll need to use it. I feed my pup on a schedule (breakfast/dinner and snack in between) and that helps me to know when she has to use it. I pad trained my baby so that she'd always have place to go in the house if needed... Dont know your schedule, but that might be an option as well... Hope this helps