Alex, let me shed some light here since this is an issue on both sides.
First, if you put a retreat order and autoresolve before it actually shows you the prompt that the ship left the battle, autoresolve counts that ship as an active participant in the battle. Same in the issue said above, if there are damaged fighter wings left and fleeing for example, a common occurrence start-game, you can auto-resolve and you'll almost certainly get them even if you could not do it otherwise. Same for example can happen when you have a super slow ship and cannot get in range of say a Hound. If you auto-resolve and you're in a sufficiently powerful ship, the game just assumes you'd win while in fact, you'd never be able to touch it.