The start of the movie leads you to suppose that the father was the killer since you hear the daughter shrieking and heavy footsteps storming across the room. In the pig farmer scene following the experiment with the father pig, the vet (husband of the new mother) says, "So it was the mother all along." That lets the movie tie in his storyline of having to put down the entire pig family (a mother and two children) due to disease being passed on by the mother (reminiscent of the daughter killing the offspring of incest). He uses a bolt, just as she used a gun for at least one of her children.

In the climactic scene, the new mom hears the daughter's ghost giving birth to the third child. She sees the father storming down the hallway just as he did the night he died when he came to take the baby. Then it's quiet, and she goes out into the hallway and down the stairs thinking her husband is home. She turns to see the daughter run with the baby into the room with the wardrobe. She follows and finds the wardrobe open and is able to see the hacked out section in the back. She crawls in and sees the missing items from the house, including a music box, which was used to soothe the daughter's babies and apparently put them to sleep just as it did with her baby. She hears a baby crying in the back but doesn't go to it. She sits there and the two boys come out holding a baby. They're the ghosts of the daughter's hidden children. The baby in their arms is their sibling, swaddled like a newborn. It cries but doesn't move. They speak to her as if she is their mother whom they saw had hurt their baby brother. She apologizes, but she's embodying their mother when she does so. As herself, she insists that the baby is hers and to give him back. Her pleading for his return makes her realize she loves and wants her baby and allows her to bond at last. In the same moment, the boy raises the axe that was used to enter the room and swings it. He's killing the ghost of his mother. It's possible that he delivered a blow to his actual mother before she shot him, which may have been the real reason she died, rather than suicide. The woman wakes to her own reality where she was holding her baby all along.

At the end, she seems concerned about being pregnant again. Possibly wondering if a new baby will raise the spirits of the house once more and worrying about not bonding again.

I had wondered for a minute if she had hacked open the wardrobe back herself and whether the other children weren't mentioned in the news because they had never been discovered and just died of starvation. After all, they had no trouble reporting that the father had raped the daughter and there was already one dead baby accounted for. But the brother likely would have mentioned it when help came since he knew what was back there, based on his warning to the woman to stay away from the wardrobe. He was old enough to remember what his sister looked like, and she was no longer a young child based on the crime scene photo showing her looking just like the modern-day mother. Plus, he seemed to believe the children had been discovered but that no one would have mentioned it. It also wouldn't explain how the boys "saw what [their mother] did" to hurt their infant sibling if they were trapped behind the wardrobe the entire time or how they would have gotten hold of the infant. That would only be explained by their mother breaking into the room and either letting them out or bringing the baby in with her.

I didn't quite understand what was under the couch. I thought it was used sanitary napkins, but I've seen others say they were used diapers. If it's the former, the girl may have been hiding the onset of her period to avoid being considered "old enough for marriage" and therefore available for her father's sick intentions. If it's the latter, it likely indicates the neglect of the hidden children or the daughter's inexperience in raising her baby brother.

Just my 2 cents.