I do a lot of hauling to/from my carrier, and I've noticed this exact issue happening every single time. Fill the cargo hold, but I don't get the "Cargo hold at maximum capacity" warning, and my ship's inventory is empty! Rest assured, your cargo is really in your ships hold! For some odd reason when you purchase items from FC's, it doesn't seem to show up in the inventory menu. If you go back into the Commodities Market/Secure Trading menu, you'll suddenly get the "Cargo hold at maximum capacity" warning AND now everything shows up in your inventory. Alternatively, just fly to the station you intend to sell items to, the moment you open the Commodities Market menu, you'll get the "Cargo hold at maximum capacity" warning, and you'll be able to sell all of the goods you purchased from the FC. This appears to be a bug with the FC's themselves as far as I can tell.
Hope that helps!