by Mr. Rothschild » Wed Apr 08, 2015 3:12 pm
On the plunder page, view HELP: How Plunder Works.
Under sub situations for losses it states,
2.If the cargo value is not enough, then the loser will either lose the ship alongside with whatever it was carrying (only if loser has more than 1 ships AND ship was not sunk in battle) or will lose any gold he is currently carrying alongside with any cargo the ship had (This can also mean 0).
This could be why, your target only has one ship.