I've been having something similar to this happening since the last update (v0.175). Docked turrets and ships vanish. They are still 'there', but you can't see them. When you attempt to change to the next docked entity by using the up/down arrow keys you get a message popup in the top corner telling you the entity hasn't loaded yet, but it never does until you relog to the game. Hit the Up/Down arrows key again and it will skip past the one that didn't load as it cycles through the docked entities. Doing a /search for the entity shows it's where it should be too, but can't be seen or used.