I don't know if this has been reported before, but if you set a ship to move between two objectives in the same place - a planet and a fleet in its orbit, for instance - and put it on repeat, the game hangs.
Also, I've got some civilian colony ships full of colonists sitting in Earth orbit after they tried and failed to load more. I know this was reported before, but is there a workaround or a fix, short of blowing the things up? It's not breaking the game, I just kinda want them free to move people around again.
Edit: Oh, wait, there's a clear orders button. Solves that problem.