In Mary's world, there are simple truths. You must always mind the fence that surrounds the village. The fence that protects the village from the Forest of Hands and Teeth. But slowly, Mary's truths are failing her. She's learning things she never wanted to know about the Sisterhood and its secrets, and the Guardians and their power. And, when the fence is breached and her world is thrown into chaos, about the Unconsecrated and their relentlessness.
Blood on These Hands / It's All My Fault: Mary continually blames herself throughout the story for her mother's death, Gabrielle being infected at the hands of the Sisterhood and Jed's implied death. Also, Jacob begging forgiveness for starting the fire that forced our protagonists to leave the treetop village months early which he thought was the reason for Travis' death. It wasn't.
Locked Away in a Monastery: Mary is sent to live with the Sisterhood after her mother is Infected. When Mary says that she didn't have a choice (after her mother's un-death, her brother kicked her out and she wasn't getting married) of whether or not to stay with them,the head nun, Sister Tabitha threatens to turn Mary out into the Forestto show her that "There is always a choice."
Mercy Kill: Jed, towards Beth. what's worse, she was pregnant. Again. Also, Mary towards Travis.
Not Using the Z Word: In Mary's village, zombies are called Unconsecrated. In Vista, they're called Mudo.
Removing the Head or Destroying the Brain: implied. It's said repeatedly that the zombies will keep shambling until they're torn apart, but when decapitated or given a hard enough blow to the head, they "redie".
Squick: some of the descriptions of the Unconsecrated are downright disgusting.
What Happened to the Mouse?: It's never explained why Gabrielle, the girl in the red vest, is so much stronger and faster than other zombies. The author hints that something special was done to make her that way, but it's just kind of forgotten about after that.
The sequels go into a bit more detail: apparently, if one of the zombies is turned when there are no other zombies around, it becomes a "breaker" or a fast zombie, in order to spread the infection more quickly. However, it isn't ever explained who Gabrielle was, or why the Sisterhood wanted to make her into a breaker, or really what any of that had to do with the plot other than letting Mary know there was a world outside. So it still does qualify as a What Happened to the Mouse?.
Actually, the Roman numerals Gabrielle left on the window pane suggest that she was a survivor from the infected village Mary and the others stumble upon later in the first book. What the Sisterhood was doing with her is a little more complicated and less obvious. In the first book, Mary enters a forbidden series of chambers, where she finds a list of names and a journal detailing accounts of infected. This implies the Sisterhood was studying the behavior of the zombies, if not outright intentionally infecting certain people to do so. In the second novel, Gabrielle, the daughter Mary named for the girl in the red vest, follows her mother back to the village of her birth. There, she finds records pertaining to the Sisterhood that imply that they were hiding the existence of survivors who came to the village in a misguided attempt to protect the people from the dangers of the outside world. With this information in mind, we can potentially hypothesize that the Sisterhood eventually decided to destroy evidence of outsiders by using them to study the infected. Gabrielle arrived at the village seeking refuge and instead found herself the subject of one of their experiments. She became a Breaker because the specific experiment she fell victim to was one where the they were studying the impact of infection under isolation.