Cloud of black smoke -- don't suppose you have a screenshot of this? The only things I can think of are alien spaceships and meteor showers that might not be instantiating themselves properly. Any mods in play regarding either? If not, might be time to try a test run with NRaas mods only and see if the black cloud...uhm, dissipates or something.

Poltergeist event's also do that if the Ghost Hunter Career is enabled. The Ghost Hunter career's hunting events and scenarios can really mess things up especially if you Reset the Town or lot during one of them cause it'll leave that lot permanently hunted until it's bulldozed and replaced it's one of the reasons I disable that one or have a copy of every community lot and residential home with the exception of the graveyard just in case a hunting happens right before I do a Reset on the Town or lot

that should have been haunted not hunted

But I what you got is a regular event just make sure to take precautions if you leave the Ghost Hunter Career enabled

I didn't even realize that ghost hunting scenarios affect community lots that way, so I would defer to sittingbear's theory over it being another party's mod. Unless you have a mod that affects those, in which case they might both be right.

There's an alien ship parked at the grocery store, and has been for a while, which I thought was odd (but I haven't had Seasons that long). (Don't have a screen shot but could take one, I guess. I think it first showed up after my sim got turned into a ghost at the haunted house?)

How do I get rid of the Ghost Hunter career? (She's not a ghost hunter; she's a street musician/professional dumpster diver.)

Which reminds me that I've been getting very odd little notes about "this town is safe from spooky stuff thanks to you" which sounds like maybe the game thinks she's a ghost hunter?

I may just kill this save and start over.

It takes a few hours for the event to pass over if the Ghost Hunter does what he/she needs too do or as I had happen once it took 2 days cause the Ghost Hunter at the time was well lazy.
http://sims.wikia.com/wiki/Ghost_Hunter

Also I periodically hear that haunted house music on some lots, and it won't go away until I leave the lot.

I don't have any mods that are supposedly relating to aliens or meteor showers. Or ghost hunters, for that matter.

You get those notices by the game when the ghost hunter does their job even if it's another sim who is the ghost hunter I could never turn that story off

Click on City Hall or a computer Nraas>SP>Town>Career Disallow or is it Disallow Career and look for the Ghost Hunter career