Like other people said, it's about your leadership points. Say you have a fleet of 1000 points, but you only have a leadership of 675, it will try to fill up that engagement with as much of one fleet as possible, and then add as much of the second fleet while the rest of the ships stay in reserve.
And while in skirmish or multiplayer battles, disengaging might not have much of a purpose or real use, apart from surrendering the match. In the Campaign, if you disengage a ship, then one of the reserve ships can come in from your starting engagement zone and join the fight.
This isn't really required the first few sectors, the battles are still pretty easy, but soon enough, you're going to be fighting larger and large battles, and though your command points will go up, it will take a while and sometimes you'll fight strong odds and you'll have to make the choice of losing ships, or disengaging them.
I recently had a fight where I had around 1100 points worth of imperial ships, fighting against a force of around 1400, and it was a really tough battle. I had to disengage two of my ships... But then the remaining two of my reserves came in and I managed to just barely win that fight.