I have recently been encountering a problem where ships are waiting at the Trading post while multiple piers are available at the Docklands.
In the first video, it appears that the ships are targeting a point just to the left of the trading post. There used to be a pier around this position, which I created to satisfy the Shopping Centre quest (see thread https://discussions.ubisoft.com/topic/109914/harbour-districts-don-t-count-toward-trelawney-objectives?lang=en-US) and then immediately deleted.
I then exited the game and restarted it (I have the exit autosave if you want it.
After that, the ships seemed to be targeting somewhere near the centre of the Docklands, though they still waited for the Trading Post to be available. (2nd video)
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I don't know how long this has been happening. I had noticed it before, but never captured it. I have a feeling it started at Game Update 12, but I'm not sure.