My first couple of Sims 4 games had this issue but not more recently.
I don't use mods. I use standard aging and don't age up babies early.
Two things I changed:
1. I have been having my characters exercise more often at all ages, like a very active character will go jogging or use workout equipment once or twice a day, a lazy one will exercise once a week or less, and the others in between. Anyone feeling energized will do a few situps or something. Characters are allowed to play with soccer ball, basketball, pool when they feel like it. Kids get to play on monkey bars or jungle gym a few times a week. I notice also that townies are more in shape now than in my first couple of games, too. I've heard that townies tend to follow the habits of your played sims to some extent, maybe others can confirm. I'm currently farther into a legacy than I have been before (gen 4 is teens) and have yet to encounter the plague of "pear-shaped townies" that people describe. The townies are a nice variety of body shapes and sizes.
2. My toddlers eat normal food and harvestables now, no more quick meals. That happened mostly because I got tired of high chairs, but these toddlers do seem to grow up in better shape. I wonder if all those quick meals maybe added up to being overweight? Quick meals can have that effect on older sims.
Or it could just be that this was adjusted in a patch somewhere along the line. Is your game fully updated?