Alex, had a weird thing happen just now that I'm pretty sure is a bug. I attacked a Pirate Plunder fleet with my fleet, because although I had fewer ships, most of the plunder fleet was not combat ready. I'm guessing they ran out of supplies or something. Their battlecruiser and most of their big ships were marked not combat ready.
Anyway when I attacked the first round, they did not choose to run, they chose to engage. I didn't think that was too strange, the fleets were both pretty powerful. So whatever, we go through that whole song and dance, he's got mostly destroyers only that battle though.. it was pretty one-sided.
The second round, literally the only combat ready ship is a single hound, who retreated from round 1. I've still got my whole fleet. I expected him to run, and for me to have to pursue all of his freighters and so on... but he decided to engage. That was when I first thought to myself, "Hmm. Odd." But I went ahead and took out his hound. Whatever.
Round 3.. .was when it started getting a little ridiculous. The enemy chose to engage, deployed zero ships, was immediately defeated as soon as I deployed my first ship, and then back to the battle dialog menu again. I did it twice more just to be sure. So rounds 4 and 5, identical to round 3; enemy wants to fight, zero ships deployed, immediate defeat. I'm losing CR gradually but really only one of my ships has dropped completely to 0%, so I'm still very much ahead.
Ultimately, although I chose to salvage after every victory, I didn't get to actually claim any salvage rights because the enemy simply refused to leave. I had to let him go. So he did.
My theory on why this all happened? The enemy fleet never "felt" defeated. It probably evaluated its tactical probability of winning based solely on fleet composition, without factoring in CR as it applies to how many ships you can actually field in the next fight. If true, the obvious suggestion is to ignore non-combat ready ships in fleets when it comes to making judgements of power.
Edit: I should note that the reason why that's my theory, is that because if you look at their total fleet composition and ignore CR, they had twice as many cruisers and destroyers as me and would probably have kicked my ass.