Hi. My sim recently discovered a patient of hers was an alien. He was wearing his human "disguise". She had twins with him but they came out with normal skin color and none of the hybrid alien feature...
are you sure the alien sim had a typical alien form? I've had a few game generated aliens who looked human even in their alien form. I've had an alien conceive while disguised and she had half-alien twins who inherited her green skin as well as some alien-specific interactions. your alien might've been bugged then.