The German side has a ned thread on common misconceptions. To date there is just a debate on the quantity of captains that can be found at any given time. It used to be the concensus that thre are always two, but that's only the case in the beginning of the game.
Other misconceptions that have already been cleared up, but may be worthy a notation are:
Piracy: you will not get charged if you attack when nobody is around and you sail the ship into a harbour other than it's oroginal home port. - Nop, we all know that charges are based on random generation and the only ways to get out is to either use save/reload or bribe at least one councillor. If no councillor is in the bathhouse of your HT make a save, [F12] until you find one, save and go back. He will no be sitting in the bath.
Prince: selling lots of goods to him will keep him happy - False. Maybe in that particular town but, Hanse-wide large-scale selling to the prince will trigger more sieges than funds in the coffers.
Please add to this list.