Ok, this is getting ridiculous.  I was not able to press R to begin to sail my ship out of port because there was another ship in the same spot.  So, I changed servers.  I take it out in the new server and now it's on top of two other ships.  This should not be happening.  Allow us to move our ships to another port or allow the ships to be maneuvered when they're top of each other.  Because of this, the hours I had intended on using to complete some missions is now gone because I'm stuck in the port. 

If you left click twice on the ship icon on the top left you will get first teleported in front of the wheel then you will grab it regardless of how many ships are piled up in the same place.

The other workaround is to swim a few meters away (in safe zone) and right click on the anchor icon so the ship moves to your location.
If you are outside a safe zone check that there is no any obstacle that can interfere to the ship.

Anyways, seems that Pearl Abyss does not shows any effort to ear us in this question because many people already suggested how to mitigate all this situation since years.

None of this would happen if players had basic manners, but as long as we have people like Rudetteo promoting immaturity by shifting the blame on Pearl Abyss instead of promoting self responsability, this is the kind of crap we have to endure.

Thanks Retteo and the like for ruining everyone's gaming experience, good job as usual.