Background: My area (Bob_Keep) is a high traffic area for new players, since there is a spot right next to it that players respawn at if they die. I have a small building with stuff to help out, and working on paths, signs, and free boats to help players get though and around my place to get to other places that have not been claimed.
It had been a few days, so yesterday, I went to check up on the villagers at my main res. I grew suspicious when I saw a baby villager, since I know I was at the max number of villagers for that area. So I checked around and found that at least two where missing, since these were ones that I purposely fenced off to keep them in one spot (one in a restaurant and on in a school). There was no way they could get out, and only myself and my wife have build permissions. After "talking" to all of my librarians to make sure that I did not loose anyone that sold key enchanting books, I noticed that some of the books offered where different, and that the one that sold Fortune 3 acted like I had never traded with him before, and I know I worked him up to where he would sell name tags. I was also missing one of my three golems.
There were also a couple gates left open (signs saying please close the gates just don't work apparently), but I don't think any of the villagers got out there. All they have access to past the gate is some shoreline and respawn zone. I also have a second village way to the SW, and that was untouched (I have a librarian that sells silk touch, and cannot loose him).
I have since worked up my librarian to where he sells name tags again, have replaced the two missing villagers, and remade the missing golem. There are less librarians then I had before, so I will move some of my other villagers to a different spot in order to get the main area to reproduce.
I have also created some subzones that I can turn damage off in to protect what needs protecting, and to leave other areas open so other players can hunt the loose animals.
I do enjoy others looking around my area, using my villages, taking care of stray animals, etc. All I ever ask is to close doors and gates after yourself, and don't kill villagers. But apparently I need to take some additional steps.