I have noticed that if I try to build a ship on a planet that has too many ships parked on it, that it crashes the game with a Buffer Overrun error message.
A lot of the times I dont have the "Launch ship" box checked so when manufacturing starships it just puts them in orbit and when the planet gets full(I am not sure how many ships that is, but there is some limit) and you try to make another ship....Crash O' Rama.
That's odd... I've encountered this, but there was no problem- when it hit the maximum number of ships in orbit, it simply halted production of new ships and wouldn't let me put any others into orbit until I launched a few.
What game version are you using? I have 1.22, so that one should be okay.