The best way to prevent that is to only remove traits with the reward potion or by using the traits.remove_trait cheat. Never remove a trait in CAS after the Sim has been played, that's what causes this to happen.
To get rid of the problem after it's already happened, use the traits.equip_trait cheat to put the problem trait back on them (cheat away one of the others first to make room), and then remove it again with the traits.remove_trait cheat instead. I had to do this with one of my Sims who was stuck with effects from the Active trait after I replaced it in CAS. And ever since then, I've only removed traits using the cheat and never had any problems with leftover moodlets.
If you don't want to use cheats, the re-traiting potion should work just as well but you'd need two of them, one to re add the unwanted trait, and another to properly replace it.
