There isn't a hygiene bar in the game. So how in heck is it that I'm often seeing NPC's walking around emitting green stink clouds? That never happens with any of my Heroes, even if they don't EVER bathe.

I believe that is from the 'unkempt' trait.

but I don't think so, plenty of NPC's with those traits do not have this happening, but then some NPCs seem to randomly get it no matter what their traits are, and even if they wash or take a bath it still doesn't go away.

Maybe it's something else, not stink? Some illness, like the black cloud?

This may or may-not be related, but I've found Sims I gave the unkept trait to would continue to generate thier stink-clouds after I removed the trait. I didn't fiddle with it much, so it may not persist after your return to the main menu.

Of course no-one seems to get offended by it either, so I'm not sure what the point of the trait is.

But then some Sims have that trait and never seem to stink... it's a bit pointless, since even Sims that don't have it don't get a negative moodlet from not bathing, unless unkempt ones don't get the positive bathing moodlet?

On the other hand, true, people in the Middle Ages were more stink-tolerant than we are!

So... what could be causing it? And how do we get rid of it? I doubt it's sickness since my wellbeing and everything else is sky high.. and it's my royal advisor has it too, I checked and she's not unkempt

That is very curious. Have you had your physician diagnose any of these sims without the Unkempt trait?

So far I've noticed three "halos" around Sims, one for sickness, one for unkept, and one for...something. I'm not sure what it is but it looks like the "Chosen by the watcher" buff, all white and holy.

My admittedly poor memory says there are slight differences between the head-aura for Plague, Curses, and Infections. They shouldn't be easy to mistake for the Green Smoke of unkept though.

Hrm. Okay... are you running any particular quests when this appears?
Are any of your Kingdom aspects marked as "low?"
What are your graphics levels like in terms of particle effects?
Have you tried clearing your game caches?

I believe that's the same halo that appears around any sim who a wizard has cast Telepathy on and it stays for the duration of the resulting "clairvoyant" buff. Still not sure why random townies are wandering around with it, though.

I have noticed that when I finish a quest, and start another quest with a different hero the "new" hero almost always has the "Bathed" buff with a few hours left on it.
It could be there actually is a hygiene motive, but we don't actually see it. And the sims on high free will automatically clear it when we aren't looking.
Hmm.
I'm going to remove all baths from a kingdom and see what happens. I'm also going to doublecheck what buffs give the "Telepathy" holy glow, although that's entirely off-topic.

But... what is causing it on totally random NPC's?

Well, I ran pretty much all of the Fame Ambition with no bathtubs or basins. Heroes still got the free "Bathed" for some reason, and bizarrely thI only noticed one sim that had unkept.

Does the problem occur if you start a new kingdom?
It might be you picked up a bug somewhere along the way, try clearing your game caches. If you're running Windows they should be in your My Documents/Electronic Arts/Sims Medieval folder.

CASPartCache.package
compositorCache.package
simCompositorCache.package

Back your saves and sims up, then delete those files. The game should rebuild them when you next start it up. I'm pretty sure doing this won't hurt anything, but back up anyways in case I'm wrong.

Unless there are other folks experiencing the issue... Sunspot flares at the wrong moment, turns a 1 into a 0, and poof: random sims get green clouds.
Other causes could be an aspect other than Well Being rated as "Low" or worse... but I have to say I haven't encountered the issue myself.

Also, if there's some water somewhere, river etc., they can bathe there.....

Just saying.

I'm pretty sure TSM doesn't have any skinnydipping.

But all my aspects are sky high, that surely isn't the issue i think