Do you know if the person who visited you has a full town of 10 villagers and also if they have an open plot?
That's a great idea to put your town into quarantine for at least 4-5 days (which is how many days of play it takes to empty your void queue). Especially so if he unboxes normally and walks around... because we have no idea what then causes them to glitch out after that. So can you make sure to not have anyone try to move out or put down any plots for the duration of quarantine? I mean, you can obviously lift the quarantine if he glitches up on you.
I am wondering if has to do with passing the duplicate voided villager to someone else (so your real villager thinks they moved) and/or opening another plot of land (so the duplicate voided villager tries to move in and the game gets confused and thinks your real villager has moved).
Btw, it doesn't seem to be triggered by TTing because just today someone made a thread that they hadn't TT'd since before inviting the glitched 2-invite villager. Their villager unboxed and walked around normally... then boom. Glitch. They had used amiibo to kick out another one of their villagers and open up a plot after inviting the glitched villager, plus did online play.