I have found some minor annoyances in the UI. I'm using the 3.9 hot fix, but these are also in earlier versions.
In all cases this is with a 1920x1080 screen with the game at 1920x1080 and the UI Size at Normal.
Annoyance #1
On the Govern Civilization screen, the Summary section on the right side needs a scroll bar. When my Net Weekly Income is at zero it isn't shown and the bottom line shows my New Balance.
When I change the tax rate to change my Net Weekly Income to a non-zero number, it appears and the Balance number is below the bottom of the screen.

Annoyance #2
If there are enough notifications, they fill the entire column on the left side of the screen.

In this example I'm not sure if the list extends beyond the bottom of the screen. I have seen long lists with a scroll bar if the list is too long, so maybe this one isn't too long.
The annoyance occurs when I have something selected and the information box appears at the bottom-left of the screen. It covers the bottom of the Notification list.

Making the list stop above the information box would be better. Also, this would be a good time to make sure the list has a scroll bar when needed.
Annoyance #3
The tool tip that shows the Galactic Ascension Status is nice, and it shows the Victory Requirements at the bottom of the list.

However, when I'm playing with a lot of races in the game, the list gets so long that the bottom is off the bottom of the screen. The Victory Requirements are no longer visible.

Since it is a tool tip, it is not possible to move the cursor onto it, so a scroll bar would be useless. It would be helpful if the Victory Requirements appeared at the top of the list.
Annoyance #4
When I'm at war with someone and go into the Diplomacy screen, one of my enemies is always hidden under the information box about me.

I can always click somewhere that doesn't have a race showing to remove the box.

I think it would be better if my enemies didn't appear on the right side until all the other places had been filled.
Annoyance #5
If I have a fleet with enough ships, not all of them are visible on the screen when I go into the Ship Report screen.

I can use the screen controls to scroll the view and see the missing ships.

I can also use the rotate function to see the fleet at different angles and click on any ship shown in the bottom row to center on it. It is possible to zoom in a lot to see details of one ship.
The annoyance is that the zoom out function doesn't zoom out enough to show the entire fleet. The screen shots were taken with the maximum zoom out. I would like to be able to zoom out more.