Fleets work fine if you assign them to Cntrl 0-9, but if you assign any group of ships into a fleet, none will attack if enemies come into range.

Outside of a fleet, carriers still retreat to gravity wells when fighters are launched, frigates, cruisers, and caps all attack at distance and safely.  But if you add them to a fleet, they all move in a group if you issue an order, and none will auto target incoming enemies.

Reproducable:  Easily.  Just add any units to any fleet.

Strangely, this bug has extended to the original SOASE as well.  I was reluctant to report this bug since I thought Rebellion was a standalone, but apparently if you use the addon option to purchase the game, it does have something to do with it since this bug didn't exist in Trinity until it began occurring in Rebellion as well.

My son purchased the stand alone Rebellion, I have the addon.  He says he has no problem with fleets attacking, but I do. Not sure if it's an addon only bug or not.

Also, on Trinity, I'm getting achievements even though that game has no achievements, which leads me to believe that these games are acting in some unforeseen conspiratorial way.  

I'm glad to say that I have not seen the Cruel AI in Trinity build Titans as of yet, thank goodness.   If I see that, I will be sure to let you know=D