I just checked again if the bug always happens and it seems alright now. If i would have to guess it happens somehow during the ship tutorial. It seems to happen when you leave the main part of the ship during the tutorial. But for some reason only once and once you replace the ship parts they stay. But the first time i saw it it happened multiple times in a row so I'm not sure what exactly causes it. Another thing which I assume is a bug is in the tutorial cave the first crafting station disappears after you progress the tutorial quest.