When upgrading your ship, you must bring the necessary number of Upgrade Modules to Penguin Pete at the Outpost's Shipyard. When the player has enough Upgrade Modules in their inventory, the (?) quest marker will display over Penguin Pete's head. However, throwing the Upgrade Modules out of the player's inventory will not remove the (?) quest marker. Simply drop the Upgrade Modules out of your inventory at a safe distance, and then talk to Penguin Pete to upgrade your ship. You can then collect your dropped Upgrade Modules and repeat the process for all subsequent ship upgrades.