Hi I've only just joined the Beta so I won't make any major comments or suggestions yet until I've played a few games.
Anyway I've only played two games so far, one before the patch where I was just trying things out and admiring the game and one after the patch to try and play seriously. As such I'm not sure if this was a problem before the patch or not (I didn't notice it before).
The problem is; that ships with auto cast abilities will try to use these abilities too much over move orders you give them. I've noticed it a bit when trying to move within gravity wells but it's most apparent when trying to jump out of a gravity well when there's a target for the ship's ability in the area.
For example, after destroying the defences around a planet I wanted my main fleet to move on and not bombard the planet but there was a Dreadnought in my fleet. It kept using its ability to bombard the planet and then moving to jump out only for the ability to recharge before it reached the rest of the fleet at the edge of the gravity well. It would turn around again and move back into range of the planet to use the ability again. It would keep doing this indefinitely and so my fleet wouldn't ever jump out because they were set to jump together. I had to intervene and turn off the auto-cast until they had jumped out.
Another example is with newly built ships rallying to a point that takes them through a gravity well with enemy ships in it (eg. a star with some pirates). I had a Command Cruiser that was total unable to reach it's destination without my intervention because it would ignore it's flight path to continuously chase around pirates trying to use its target acquisition ability on it.
These are just two example but it seems to happen with any ship that has a target for one of it's abilities. It's more noticeable on some ships than others because of how often they'll meet valid targets, how fast the ability recharges and how slow they move.
If a ship is given any kind of move order then it should prioratise that over everything else. It should only attack or use abilities on targets that happen to get into range of it's flight path. They shouldn't run off after every potential target they see and forget where you told them to go.