lol i figured it out... All the ships in my empire happened to be either the vasari missile frigate or the anti-fighter frigate (also uses missiles). And i had just finished researching Charged Missiles, and for some dumb reason (ai bug?) they all constantly activate their charged missiles even if there are no enemies in the system, or even if they are not within range to fire on the enemy..
Had to manually turn off autocasting for each of the 100 ships, OUCH! I'll never research that again 
This is with Sins 1.12
