Hi Sami,
I was trying to think of what exactly triggered it but nothing comes to mind. I can rule out your three ideas though, I only very rarely save scum and wasn't doing it at the time, I don't think the game has ever crashed on me and I wasn't force quitting either. It hasn't happened to me again so far but I'll try to pay more attention when it does.
I have since come back to a village where this happed and the item in question (it was a sickle) was there on the ground with the unpaid marker, I picked it up again and dropped it but nothing changed. I also tried buying it from them but this time they didn't even charge me for it (as in, they didn't believe I had anything of them in my inventory when I talked to them), I think it might be because when it happened originally I wanted to leave and they ran after me to demand payment, so I just told them to take the item back - at the time it wasn't in my inventory of course but there on the ground where I had left it. Oddly enough, when I now intentionally try to leave with it in my inventory, they still recognize it and come running again. Also when I try to just give it to them (deliver items) they recognize it as not being mine and refuse.