Hey, I've begun having this problem partway through a game I'm playing. I seem to have had a variety of glitches where ships don't listen to my directions, but I've isolated this particular one and captured it on video.
Problem is, my ships don't follow my attack orders. By default, they attack their target for a little while, and then get "distracted" and go attack something else, sometimes changing their reported attack order to their new target, and sometimes not. If I disable Attack auto-cast (as I did, thinking that might help fix the problem), then they attack for a few seconds and then stop.
Here is a video of the problem. First I show what happens with Attack auto-cast disabled, then what happens with it enabled. Unfortunately the quality seems to be pretty low, so it's hard to see the red attack lines.
(This bit might be a red herring - but it seems to happen when my capital ship's Detonate Antimatter ability is used, and when its effect ends.)