This is the reality of the current effect of the Executive orders regarding passports for trans people in the US. Because of the way things are implemented they are getting stuck in a no-mans land where they cannot have any travel papers at all. If you know a place to share this please do.
From what I’ve heard, his EOs have caused massive confusion and stuff is getting stopped because government workers aren’t sure what the new rules actually are. I would tell your friend to try again in a few months.