There was some analysis done in an earlier thread which suggested that the benefits gained diminish with each Trade Ship added to the stack. As a result of reading this I try to limit the number of trade ships I place on each Trade Port to five.
Also as Mr.Alphonse has already stated when adding (or removing) ships from a stack, make sure you move the stack off of the Trade Port (the circle) first, adjust its composition and then move it back. Trying to add or remove ships to a stack whilst its on the Trade Port can lead to weird results. At best you will suddenly stop receiving any trade from that fleet, and at worse the fleet will become useless and locked in place so you can't do anything except scuttle it to free up the Trade Port.
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