The companions being alive is by design. There should be a dialogue option something like 'didn't you die on the ship?' but I don't think that made it into the last update.
The Void-zerglings not attacking is an issue, though. Do you have a save before that point?
If so, please email it (or a Dropbox or Google drive link, etc) to supportdos2@larian.com, with a description (or link to this discussion).
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'.
