Aha! So it's not just me. One of my non-updated towns that has never been online and has never TTd, has Merry lurking on main street for a long time now. She has never been a resident. I am very meticulous about keeping track of events and villagers. When a new town is started, I write down those 3 who are with Isabelle at the station and the other 2 on the way to town hall. Written down in order are all new arrivals. No way she could have slipped through. A brand new cartridge shouldn't contain such an oddity. Nintendo must like playing mind games?
I've had Villagers on main street that I don't remember having in town. I always assumed they had snuck in and out while I was on a break from the game. It still seemed strange though because they must of been super quick about it.