I built a prison/commune iron farm under my house months ago, I play nearly every day.  21 villagers with 21 beds & 21 workstations.  The villagers can roam around the enclosed space, it is about 10-12 blocks below the surface, it is completely lit up and completely sealed from the outside world.  I logged in after a couple days away, I then captured a zombie villager that had spawned near my house and brought it (in a boat) to a closed cell on the other side of a one block thick wall next to my iron farm for future healing/discounts.  I noticed as I wrapped up for the night that the population was down to maybe 18 with 5 as babies, some villagers had despawned, which I know is normal.  I log in the next night, when I entered the iron farm I was immediately attacked by 5-6 zombie villagers, which I killed.  There are no other villagers left.  The original zombie villager is still in the boat in his cell, there is no access to the cell from the iron farm.  Like I said I have had this farm for months, I used to have skeletons spawn so I truly lit it up and have had no mobs spawning for months.  The boat is right up against the wall dividing the cell from the iron farm.  I figure that had to be what started all of this: the zombie somehow killed a villager through the wall and that villager turned into a zombie who killed another and it was a chain reaction?