Here are a few small things that bug me, hopefully the devs will add them to their to-do lists:
1- Cap ships auto-bombard after everything else (or almost everything) has been destroyed in the gravity well, but if a single vessel like a scout enters the well the entire fleet gets distracted and runs after it - not even catching it in time to destroy it. This is very undesirable. It means you you have to manually select each cap ship and tell it to bombard, every single time. I suggest a change that gives all ships, but especially bombardment capable craft a sort of "default attack priority list", with planets being at the top of that list when there are no significant threats in the well. A scout should not distract an entire fleet from bombarding a planet.
2- In the same vein, many times ships will sit idly by their cap ships while they bombard when there are still enemy targets in the well to destroy. They should be set to destroy all enemy building and ships by default.
3- It's the distant future, yet ships still don't know how to avoid static defense items when moving through an enemy sector. It would be great if ships would simply go around the attack radius of cannons rather than flying right though them, or at least have this as an option.
4- I'm still seeing the problem where a single ship from a fleet will sit on the edge of the gravity well doing nothing, even if a battle is raging only a short distance away. If you mouse over the ship it says that it's going to jump to another sector, but it never does. Sometimes it doesn't even say it's jumping, it just sits there.
5- If you build more than five frigate factories in a system only the first five produce the frigates, no vessels come out of the others.
6- The voice over "Our Planet is under siege" occurs when almost any type of any unit comes into the well, event if it isn't attacking anything. This is more than a little annoying.
7- Sometimes the AI will continue to spend money on Pirates even though the Pirates have been destroyed and you and a single AI are the only players left. This is an obvious bug that needs to be addressed.