A few people have reported this problem. One person said they reloaded a save after the fight with Alexander, and when they headed to the Lady Vengeance the second time, they didn't have a problem.
Please email supportdos2@larian.com, with a description and your latest save (or a Dropbox or Google drive link, etc), as well as one just before heading to the ship, if available.
Each save is a folder in the '..\Documents\Larian Studios\Divinity Original Sin 2\PlayerProfiles\<ProfileName>\Savegames' folder. In Windows Explorer you can zip file(s) and folder(s) by right clicking on it/them and selecting 'Send To | Compressed (zipped) Folder'.
