From the Creation Kit wiki:
Bugs/Issues
There is currently an issue where created actors do not export their facial data (scars, make-up, tones etc) onto the rendered NPCs in game. This can be temporarily rectified by opening the console and selecting the actor in-game, and typing "setnpcweight x" for the selected NPC. However, this only sets the skin tones to a normalized state, with no facial traits.
I REALLY hope this is something Bethesda is planning to fix with a patch, and not one of those editor bugs that they let hang around for years like the LOD generator.