I'm having this issue too. Can't figure out what caused it. It seems to be some combination of mods, but once it happens I have to disable everything and start over. For example, I was doing the marriage quest and after completing the ceremony, my wife just stands at the altar. She went through the script about moving in, we settled on a place, and she never left. She acts as if she's in our home. She'll cook, give me money from the shop, but she's in the Temple of Mara and will not budge. I tried killing her with the console, but she's essential now somehow. This happens with each bugged npc I've noticed. I can't kill her, attacking her only downs her. Bumping her, waiting, nothing works. I spent hours earlier today trying to find the mod culprit but I can't. I disabled everything, it worked fine. I started adding back armor mods. Then lighting and graphics, then gameplay tweaks. It seems to be something like Unlimited Bookshelves, a Dance with Death, Dovahkiin Relaxes, but disabling them individually didn't fix it. I tried removing all of them again and it still didn't work. I'm so fed up.
