I'm finding that with Pirate Plunder Fleets, the AI thinks the Freighters are combat ready, so they try to Engage even if they are the only CR-viable ships left. This is usually the case after a fight since the AI keeps them in reserve during the initial battle phase. However, when I re-engage the Freighter-only fleet (along with the mothballed ships it's transporting), the AI doesn't deploy ANY ships at all. I have to deploy at least one combat capable ship to get the "Enemy Defeated" message (sadly, tugs don't count.) They will continue to do this on engagement unless I leave or I harry the reserves after each engagement until their CR rating is below deployable levels. This is a waste of my fleet's CR rating since I have to deploy a ship to harry them low enough to actually fight them. Letting them go and intercepting them again produces the ENGAGE > NO DEPLOY > DEFEATED > HARRY cycle again.
On a somewhat related note, I've noticed that sometimes, freighter CR ratings aren't displayed at the dialogue screen. I'm not sure if this is a bug or if their CR rating is so low that it takes 2-3 harry's before their actual CR rating falls below their max CR.
Both cases involve the Tarsus freighter, if that helps.