Bugs:
B1. I find that ship build completion notifications are not always presented. I find ships that were built but not launched, especially after reloading the game. I have also found planets not building anything for the same reason.
B2. You can crash the game by deleting a ship with "Name1", then immediately creating a ship with "Name1".
B3. When moving a ship from a square with other ships in it, the ship moves away, the selection highlight moves with the ship, but the panel at the bottom of the screen stays on the ships that were left.
B4. I use the "Civ Manager:Colonies" list to examine a planet. I go back to the main display. I select a planet, and examine it. When I press "Done", sometimes I end up back at the "Civ Manager:Colonies" list. This will happen for a while, and then something clears the condition, and proper behavior returns.
Interface Annoyances:
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A1. When naming a ship, you do not know what the existing names are, so you have to remember them.
A2. When creating a ship, it is impossible to compare the design you are creating with the characteristics of existing ships.
A3. It is difficult to find the list of components on an existing design. The only way I have found is to "D" on a ship of that class. But I cannot do that for a design that exists.
A4. Due to the HP gain from experience, it is clearly in your favor to upgrade a ship. However, the process of upgrading ships is a pain. And finding all of the ships of a given model is difficult. Especially if they have been through an upgrade already and their name no longer reflects their class.
A5. When selecting a research technology, I only can see the name of the benefits, and what they apply to. I am forced to remember what the benefits of that upgrade are. Some are obvious, some are not.
A6. It seems to be impossible to upgrade a ship that is sitting in a square with other ships. You cannot give orders (upgrade, sentry, etc) to a ship with other ships in the square.
A7. The planet details screen has a "Done" button on the far right, and a "Back" button on the far left. I find that "Done" was usually what I didn't want to do, and "Back" is. However, most of the other screens have all the buttons on the right, and it took a while for me to train myself on this. This is especially annoying when moving through each colony in turn, and you look at the details, then lose your place in the colony rotation.
A8. It would be nice to have a ship list similar to the "Civ Manager:Colonies" list.
Economic annoyances.
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E1. I cannot build an obsolete, but much cheaper, Factory. This means that new planets, or newly occupied planets, will take much much longer to become useful, or I am forced to buy the latest manufacturing plant, at a much higher cost.
E2. I cannot focus a planet on a particular task without rebalancing my entire economy. I find the global economic settings to be quite restricting in behaviour. Example: I have created a research colony. It is not much good for anything else. And I have created a production colony, with a star port and lots of factories. The two conflict in the global requirements. The restricted number of squares on a planet force this kind of specialization, but the overall economic model interferes heavily with that specialization.
E3. The level of micromanagement can be very annoying. Frequently, I must go through every colony, and make sure everything there is set correctly. This does give the AI an advantage, because they don't get bored by detailed micromanagement. I find that the game wants a high level of micromanagement, but the interface does not make that level easy. This becomes extremely apparent on a gigantic map with lots of planets. Which may not be the "design" model for the game, but by being extreme, it helps make some issues more apparent.