Cannot comment on in-game issues but I have the same problem with Alien Kids in CAS.
The game seems not to be able to save the hair colour of alien kids but instead randomizes it each time you change certain things/or when certain events occur.
Here's what I experience in CAS:
1) Create a random alien kid in CAS. Choose a hairstyle and hair colour. Click on save household and randomize the picture a few times. The hair colour changes randomly when you randomize the picture. Also the hair colour in the "family portrait" is usually different than the hair colour in the "individual portrait".
2) Download the household from "My Library" into CAS usually results again in a change of hair colour.
3) Switching between sims in CAS every few times results again in a change of hair colour. (Just create a couple of alien kids and switch between them a couple of times.)
Some hair colours seem to be more affected than others in certain cases. For example the blonde hair colour seems to stay often in case 1) but not always.
No mods/cc. Restarting/repairing the game doesn't help.