Yea, this bug just ruined my game and I can't get through it...
I did not even realize why the orphaned shipyard button appeared, as I built no shipyard at all around that time. The shipyard have disconnected itself without my order and my planet displayed a just started shipyard build, while I couldn't get access to the planet, dunno why. Of course there was no way to avoid the crash every time, no matter what I did with the shipyard... so bad. I think it has nothing to do with the station buildings, neither the increasing number of planets, because for that reason the bug could have occurred many turns before. (I did no shipyard build, nor acquired a planet around this time, no colonize, no invasion, I was only moving constructors and set up planetary buildings. I didn't even touch sponsoring things.)
It must be mentioned however, that this whole station stuff is just broken. If I move a shipyard then start to build, sometimes the ships just stucks in NA time and they are ready by the next turn, like if I purchased them. The opponents also release a ship every turn if a station gets NA time, even if they not moved them. Then the AI stacks up hordes of supports ships into one tile which renders the opponents useless - too easy to conquer.
By the next patch we must have an option to manually destroy any shipyard or starbase as there is no way of getting rid of them. Even if this doesn"t solve the aforementioned bugs that are critically game breaking. Now I need to start a new game only hoping this won't occur once more, but it can any time.
Edit: Ok, this is also weird. Somehow my planet was taken without enemy troops around (I can see the area) nor by influence, yet close to the borders. I can retake it with my troopship again, but not attaching back the station. Now if I click on any station's sponsoring button (as I tried to switch things up seeing if it works, or unanchoring to move around) the game still crashes, there is no possible thing I can do about it. :/