While in the shipyard screen, it is possible to build a ship by double-clicking on it. When this is done with missions, sometimes the mission is built, and sometimes something else is built. When something else is built, it is usually whatever is first in the list because the default selection when entering the shipyard is always whatever is first in the list. If a different ship had been selected after entering the shipyard, it will be the one built. Normally double-clicking will select the desired ship then add it to the build queue. For missions, double-clicking doesn't always select the mission before adding to the build queue. As a result, the ship added to the build list is the one previously selected, not the mission.
The solution offered by Stardock is to always single-click on the mission to select it and make it appear in the view screen. It is then possible to double-click on it to add it to the build queue. The only problem is that single-clicking doesn't always select the mission, so it is necessary to click more than once on occasion.
While playing recently I found the cause. The way ships are listed and the way missions are listed are different. See this screenshot.
The right side of the information is different for ships and missions. Ships have a hourglass and build time, and there is no tool tip for the build time. Missions only have build time, and there is a tool tip for the build time. Single or double-clicking anywhere in the ship information that isn't next to the scroll bar will work. Single or double-clicking anywhere in the mission information that shows the tooltip doesn't work, unless the mission is already selected. The game doesn't respond to clicks in the area of the mission information the causes the tooltip to show, unless the mission is already selected. I have added a green box that shows the approximate location in this screenshot.
Single or double-clicking anywhere on the mission outside the green box works. It doesn't matter if the mission has already been selected or not.
This can be easily seen by starting a game as a race with more than one planet in its starting system, like the Terrans, settling a planet quickly, then choosing the Colonial government. That allows missions to be sent. It should take a lot less than the 15 turns it took me.
If the layout of the mission information can be changed to match the layout of the ship information, the problem may be eliminated.
This isn't a big problem, but it exists because of a lack of consistency in the UI. Now that I have found the reason and the way to avoid it, I don't think I will experience again. I'm reporting it so that others having this problem will know how to avoid it and in case some one wants to put some effort into fixing it.