This error still exists in build #1890. While hitting "Exit" moves player out of Phoenix and back to their own ship (instead of the Hangar as one would expect) both the scenery screen and the menu buttons don't update. Opening Codex or Save menu forces screen refresh, allowing a crude work-around, but the player unaware of the nature of the bug (and the workaround) will be likely left stumped.
Attached a current version savegame; to reproduce: click "Hangar" -> "The Phoenix" -> "Exit"