Yes, this happens a lot. The chins, jaws and shoulders of sim children seem to live their own life, despite how the parents look. Children often get their own, hardly existing chin/jaw or narrow shoulders even if the parents certainly don't have those. From teen age and upwards, is when you can see it clearly.
Would you be able to tweek the genetics mechanisms, or is it written in stone how the game genetics work? I mean is it still possible to further develop the genetics? In that case I suggest that you make children inherit either their father's or their mother's chin, jaw and shoulders. As it is now, all these three get smaller and smaller for every generation and after several generations of playing, the sims have extremely small chins, pulled back jaws, narrow shoulders and a pear shaped body. The game should obviously never give body parts to a child which neither parent have.
The skin colour genetics don't work either as you have divided the colours into 3 colour temperature groups: warm, neutral and cool. If parents belong to different temperature groups, their children often don't look like either parent or any mix between the two, but instead they get a skin colour far off from both parents as the temperature groups run on different scales.
The pear shaped bodies that seem to get more and more abundant the more generations you play, likely comes from the fact that you allow boys to inherit their mother's hips and if the mother has broad hips, the boy can get it too. Then the boy in turns pass it forward to his children. I think you should avoid hips to be inherited from mother to son but rather from father to son.
You need to fix the genetics, it's not working well and you need to try to merge the skin colours into one scale like before, which step by step go from very light to very dark skin coulour. This way there will be no clash between the mother's and the father's skin colour but any colour on the scale between their two colours should be easily picked up by the game mechanics so that the child's skin colour will be either of their colours or a mix of the two, thus any shade in between.