This is still happening, but yesterday I had THE weirdest, exact opposite problem, and food seems to be the culprit. My sims have been max-fat on age-up to teen as an unwritten rule for ages, and will often be perma-stuck at that weight without using cheats to edit them in CAS mode. But yesterday I had a toddler (Jace) with a mother who has the "health nut" lifestyle trait and decided to experiment with feeding the toddler "healthy" meals out of the mother's available cooking list. Then as a child, Jace ate only about a handful of those healthy meals and otherwise ate harvestables because their garden produces a ton of edibles. I think he spent a week and a half to two weeks in child mode, and then I aged him up to teen. Immediately I could see that his waist is so thin it's cartoonish and he has muscle tone on his arms and legs which makes him look even more like an hourglass-gone-crazy.
My guess is the game is doing some kinda calorie math with normal meals and possibly even "quick" meals from the fridge, and toddlers/kids should not be eating the full meal but they do anyways because the hunger bar works the same regardless of a sim's age. I can't say for sure if the healthy meals affected Jace as that would take more experimenting with future kids, but I'm going to guess the harvestables made a huge difference because eating harvestables with adult sims seems to help them keep slim even if they don't exercise. But yeah... Jace literally looks like he... skipped abdomen day? And is missing some ribs to boot. It's that bad.