Two of my sims just had a baby. One of the parents have green eyes dominant and recessive (according to SimPE), the other has light blue dominant and recessive. However, their daughter has brown eyes even though her genetics codes show dominant light blue, recessive green.
Have any of you experienced this? Im not necessarily looking to fix it, she looks real cute with brown eyes, just thought it was an odd error. It makes me wonder if she's gonna pass on brown eyes as well despite her genetic coding.

Sims have two values of eyes, and can carry co-dominant or recessive genetics for several generations, so it's entirely possible they can get a different eye color than their parents if the parents transfer recessive or co-dominant genes to their kids for a different eye color. Babies should get one of the two genes from each parent, though - and I'm guessing the parents were from CAS since they had the same eye color for both genes.

However - if the eyes look a bit different from the default eyes you have, it could be the eyes are geneticized ones lurking in your downloads. They essentially are CC but work like extended default eyes, so they can show up if the parents have different colored eyes and the genetic value for those eyes are in the range that pick up those particular geneticized eyes. Since these are numbered and strictly not color-coded, they could be showing up with the "wrong" color if the creator used a somewhat different system, and they can also show up even if you haven't put them on the parents. If you don't think/know you have geneticized eyes, check downloaded sims and eye downloads (the eye creator usually says whether they're geneticized or not, but not always).