There are a few things you can do:
Click the auto-turn button on the system map, this will have the game(in most cases) go through turns until something happens.
Force set number of turns above the auto-turn button. this one is dangerous, but if auto-turn isn't working it will force the issue, so you could say force 12 turns, click 5 seconds, and it will advance 1 minute for you(regardless of what happens in that minute so be careful).
Space time bubble: turn sm mode on, bring up the system map, and go to the contacts tab. there is a check box for a system wide time space bubble. this will halt all processing outside of this starsystem, so that you can fight without other events taking up cpu cycles during the fight.