Yes, just happened to me too. I don't use any mods or cc either. Today one of my other Sims in the household aged up, so I gave her a post-birthday makeover in CAS. I think that's what triggered my alien to have his disguise broken. I noticed that he was in his alien form, and I thought I left him disguised. He was in disguise, but his human and alien forms/outfits were now identical. He's my first alien born in-game from an alien abduction. I don't think I could recreate his human disguise if I tried!
The work-around that I used was to go back to a previous save and move my alien out of the house. Luckily I had saved before I went to Manage Worlds for the birthday makeover. Then I changed the birthday Sim's outfits the way I wanted, went back to the game and invited my alien to move back in.
Of course, moving him out and back in again messed up my household collections, but that's a whole other bug and I'm too tired to go fix that now.