I am playing as the Phalenoids Advance and I have researched Sovereign Immunity (first screen snapshot below), but I cannot assign a leader to the Due'Celes command ship (second screen shot below).  Usually, at the bottom of the popup that shows the properties of the ship, it will say what you need to research to be able to assign a leader to the ship (third screen snapshot below taken before I researched Sovereign Immunity), but there is nothing there now.

Here is a link to a save file that should let you see this:

https://www.dropbox.com/scl/fi/k5tnr0i3mohqage58p8je/CommandShipIssue.GC4Sav?rlkey=yk1lzy04rskimj07hyhfzxx88&dl=0

Steps to recreate:

1. Load the save file
2. Click on the "Leaders" icon in the tray at the bottom of the screen.
3. Click on the "Commanders" tab
4. You will see that 3 of the command ships are disabled for no apparent reason