On Xbox One S so not a mods or CC involved issue here, but I promise that I've noticed this firsthand before personally in the past, and unfortunately many Simmers won't report this because they haven't noticed like I have it seems, if the game chooses an alien already in their disguise form they lose their alien form completely while oppositely if they're in their alien form their genetics become that of a randomly generated Sim and don't keep the disguise they already had before the game turned them human, if that makes sense.
Edit By Crinrict: Added Tag to Title, Adjusted Title