Ideas
I'm also seeing this in my save but it wasn't just a visual glitch for me. The Neutral Confidence trait was all that showed through childhood even though she walked around with a confident moodlet most of the time. When I aged her up a little early via the birthday cake she did NOT get the High Self-Esteem trait. That truly surprised me because I decided to age her up before the actual day for a birthday because she had already completed five aspirations, was an A student and confident most of the time. I was ready for her to move on to high school.
The only thing I can think of to account for her not getting the High Self-Esteem trait is that I aged her up early, rather than waiting for the game to tell me it was her birthday. This may have been visual only for others but that's not my experience.