You don't say much about your setup, so I'm guessing here, but I *think* all you need to do is go around all your ships before you end a turn and make sure that none of them are on courses that are longer than their per-turn movement.

When you're zoomed in to the 3D level, you can see the time remaining for a given destinatino point (pulsing blue thing).

If you're talking about post-reload spontaneous course settings, switches to auto-explore, or switches to auto-kill, that's a new one for me, and it sounds like you have a configuration problem or have found an unusual bug.