As you change your transport orders look at the information under the ship icon on the right side of the transport screen. The ship represents the total number of cargo holds in all the ships your Empire owns. Each cargo hold can be used for only one item each turn.

You see that as transport orders are increased cargo holds are moved from the trade number and allocated to the transport number. If you reduce transport orders more cargo holds are allocated to trade. 

If you run out of cargo holds you will not be able to transport more commodities by water and you will have to select those commodities you want to receive.  

Generally, if you have available resources or materials to transport, and unused labor on your industry screen, you should construct additional vessels for your home fleet in order to make use of all the commodities in your Empire’s transport network.