When I want to sell my Odyssey ( settlement materials ) at my carrier, it says I have no stock of any of those items... and if i look in my inventory in the ship, they are all there... how 
Your ship is still mass storage for on-foot mats, items to be sold have to be transferred to the Bartender's absolutely minuscule (max 100 units for sale) in-stock locker. Should at least quintuple that stock max.