You should do this
Remove all your skins and mods and custom content. Then start a new game and put your family in the new game. Then try what skin you're getting.
Vanilla means = without flavor = no mods, no custom content, no custom anything, Only plain EA = plain vanilla.
Just had this happen as well. Too lighter skinned parents had a dark skinned baby girl. I'm not using any custom content and am using the base game only so it's definitely a Maxis issue.
Is it just darked skinned as baby or also as a child ? There's another issue but it only affects baby so maybe you could age up the baby, check if it it's both and then exit the game without saving (save before the aging up)
