I've seen two sources for such things in "normal" Sins:
1) Fleets phase jumping (they should jump grouped together but won't ever do that). If I order the first ships to attack, all ships who did not yet initiate the jump will later also attack, but all ships which are currently jumping will simply MOVE to the enemy ship without fighting! HORRIBLE BUG!
2) Ships with special abilities often have very low attack damage. I haven't yet found a way to manually FORCE them to attack. Indeed, they ignore attack orders and thus even split the fleet (if there was an old command to leave the system) or try to MOVE to the enemy ship peacefully. If I leave them unattended, they do auto-attack the enemy. My workaround is to always give first a move order shortly ahead of my fleet and then the attack order. That's wasting much time!
Both is highly annoying. Any solutions?
Screet
