When you swap servers or characters on a ship the ship is partially sumerged when you load in on the character with the ship. This appears to be somewhat mitigated by not being mounted to the ship, so it may be related to the character and ship registering as a single entity initially when the player loads back in.

Not a bug... it's a feature! it's there dor years... so one must assume that in some parts of the ocean, you have big waves!
Look at picture in answer #8 here: https://www.naeu.playblackdesert.com/en-US/Forum/ForumTopic/Detail?_topicNo=25586