Traits not disappearing after removing them? Bug?

Try removing all off the traits that the sim originally started with and all of the traits they currently show as being listed as having (even if you want to keep them remove them just to get a clean slate) and then re-add the ones you want up to 3 traits. I'd suggest doing a google search to find out exactly what they're called in the game because they do sometimes have different names.

ETA: Looks like you got it figured out so yay for that!