I'm so glad this isn't just me. 😭
I have been having this issue a ton and its so frustrating and disappointing. Especially if one parent has really distinct facial features and its their face copied onto the kids.
Ex: Neighborhood stories generared another son for the Goths that looks just like Mortimer, which I thought was cute at the time. My legacy sim (male) ended up marrying this mini-Mortimer. They had two kids, a boy and a girl. Boy had the legacy face, girl had Mortimer's face. Continued with the girl and she married a sim of mine that had a very round face, opposite the thin sharp features from Mortimer (I was hoping they would balance out). They had twin girls, both with Mortimer's face, and a younger son, with the dad's face. Mortimer's face on all the women of my legacy is rough... (I'll try to remember to come back and add screenshots.)
It was super noticable in that save because Mortimer's face is so distinct but is definitely happening in my other saves too. My 100 baby mom makes so many little clones of herself.
Skin and hair colors end up somewhere in between the two parents and occasionally a single feature from the other parent might get swapped in. Like if a kid got all of Mortimer's face copy pasted but swapped in just Bella's lips, eyes, or nose.
(I'm on PC and do have Mods. The only one that has a shot at impacting this is MCCC but I don't think its to blame, especially since others here are reporting the same issue with no mods.)