I've had this happen several times.  It happens when a space monster destroys the commander ship.  This causes a new space monster infant to appear.  For some reason, probably a bug, the commander gets transferred to the infant, and they both appear in the list of commander ships.

You can still interact with the commander.


In your case I was able to gift the commander a harmony crystal.  I think that would be a stupid thing to do, but it can be done.  Even better, I was able to fire the commander, who then appeared back in the unassigned leaders pool.


The leaderless infant vanished completely.

You can do all of this if you want to.

I'm working on getting a save before the space monsters destroy a commander ship to see if it happens all the time or a lot or rarely.  I've finally found some space monsters and am sending some commander ships to them.  After they get there, I'll see what happens and go from there.  I hope I'm able to get a save where it consistantly happens so I can submit a bug report with it.  If it happens, it will be submitted on Discord.