Have you ever caught a whiff of a positively charged conditioner like Incroquat BTMS-50 or honeyquat and wondered why it smelled fishy? There's nothing wrong with the product: You're smelling the ammonium salt in the cationic quaternary compound! (That N in the molecule above...) Some people can smell it, some can't. It's hard to know if you'll be a smeller or not until you get a nose full of the ingredient.
It shouldn't remain in the finished product, although there are some very sensitive noses that might still notice it. If you do, consider scenting the product at 0.5% to 1% to mask it.