Hey there!
First off, I'm not sure if this is the right forum to post this in, so feel free to move my post if needed! 
Now as for my problem, I cannot remember if this happened in other versions of the game, I have the latest patch, or if this is a new change, but I find it to be very annoying. Each race has an ability of some sort that prevents an enemy ship from moving or attacking, one that is most commonly used on capital ships for good reason. The problem I'm having is that if I tell my fleet to jump back to one of my planets, but on the way my capital ship gets hit by one of these abilities, my order gets erased from its cue and when the ability wears off, my damaged capital ship auto-picks a target and ends up getting itself killed if I don't watch it and keep re-ordering it to jump every time it gets hit with the ability. I've lost a couple of ships this way and I think it's pretty annoying as when I've told my ships to retreat, my focus is usually elseware until they arrive.
I'm not sure if this is intentional or not, but I would prefer it if they kept their order que even after they were hit with those abilities.
Thanks for listening lol! 