Thanks Meph.
The workshop issue was a mason's workshop and a carpenter's, and just building beds, doors, etc. I didn't see any pattern to when they disassembled in terms of it was idle or not. I believe they were built with wood once, and shale too? They disassembled multiple times. Though there was a mechanic's workshop next to them that was not disassembled.
No fog/mist that I noticed, only rain. No mages or other creatures. There was a worker hornet in the room with the farm, which may have been the cause there? But I'm fairly sure they came after I had the mason/carpenter problem.
I'll keep an eye out for it happening again and see if there is a pattern to it.