To get extra goods from a ship than it is supposed to have, you need to be able to leave the city and go to the Bayou. First, however, load a ship up with a particular type of goods. Then, send it to another port, at which point you should exit the trading menu and head to the Bayou. Once there, return to the city and access the trading menu again. Now, your ship should be in the port regardless of the amount of time passed, and, when you select to trade and sell goods, you will see three complete sets of goods, instead of just one. You can do this with as many ships as you like.