Probably silly question: are you actively playing the household where the bugged infant lives when you try to achieve milestones?
I ask because I have a sim who got an NPC sim pregnant without me knowing (through mods), then got a girlfriend, got engaged, got her pregnant, and eloped all before his first son was born. You know, like sims do.
Anyway, the first son lives in a household that I don't actually play with his single NPC mom. Wanting my sim to be a good dad, once his first son hit the infant stage, I started having dad invite his son over to hang out (don't ask me how that works; he just talks on the phone and then his infant son appears, alone and unable to move, on a little placemat on the curb). Further wanting to be a good dad, I decided to try to work on infant milestones with son #1 while he was visiting.
What I discovered is exactly what you're describing: the bars say he is making progress towards milestones, but he never actually gets them. Since it was my first ever experience with sim infants, I thought it was just infuriatingly difficult to get these milestones, until son #2 came along (this one is actually part of the active household) and the milestones came like butter. So, it seems that when a sim is not part of the active household, they cannot unlock milestones no matter what.