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).

What minerals are Maintenance Supply Points made of?

1 MSP = 0.1 duranium + 0.1 gallicite + 0.05 uridium (0.25 total minerals)

Probably from this thread. I don't recommend that thread simply because it's not official and is therefore unsupported, but I've used the mirrors once or twice myself so it's a viable alternative.

Thank you, nuclear!
The important thing is that the resulting installation is reliable.