Can you provide a save game that reproduces this?

Worked for me last night.  Fleet was at 6/10, then added commander.

Version:  Current opt-in with all DLC.  No mods

Thanks for the save game. You're right, the 3.6 update introduced a bug into the United Earth ship style such that a commander ship can't be created. Your faction is using this ship style, and so being affected by the bug. Sorry for the inconvenience, we are addressing it now. This issue should be limited to the United Earth faction and custom factions based off of it, so you should be able to assign commanders when playing a different faction.

Commander cannot be assigned is NOT limited to United Earth faction............

I have one with Drath, I mentioned it in discord but can't post there due to file size

As I also said in discord something that may or may not be related, I got the Commander tech through a trade prior to being able to research it, ie I didn't have the tech directly preceding it in the tech tree but got it caught up later. You can see in the game save it has the same "no room" tip hovering over the disabled assign commander button.

https://ufile.io/82pig

Possibly unrelated and in the same game save as posted above, cannot create a commonwealth, "Missing Data" name your new faction etc messages and no matter how many times I try to name it, it keeps popping the dialog.