You can select a commercial fleet as the target of your new fighter production. It seems a 'dangerous' and totally un-necessary option to me.

The USS Endeavor, an old space shuttle converted to an assault ship, being launched by the Dreadnought USS California of the 1st attack fleet, tries to board the enemy raider Bonaventure at 8000Km/s, disabled years before during a space battle between carriers.

I knew it was somewhere there, floating out in the space, just waiting for my special forces.

If I name one manually, will he stick, as some officers do when you name them by hand?

No, you need to turn off auto-assignments or disable officer assignment to the fighter class(es). That said, it's not worth worrying about unless you find yourself lacking for XOs generally because your fighter wings ate all the officers.

What minerals are Maintenance Supply Points made of?

Complement to nuclearslurpee info, if you don't remember, you can off and on the maintenance facilities on a planet and check the planned minerals expense variations.

This is not a bug, this is how automated assignments work. The command module jobs like XO are usually considered to be lower-priority than ship commands, so when a new ship command opens up (from construction, deaths, etc.) it is likely that an officer assigned to a subcommand job like XO will be reassigned to a ship command role.

One common cause here is if you are building a large number of fighters which do NOT have the "No Officers" checkbox ticked in the class design window. Fighters tend to be built frequently and take your low-ranking officers out of subcommand positions so they can command the fighter - I usually don't let officers command fighters because of this (and because having a LCDR in charge of, like, three guys seems a little silly to me).