My theory is that the doctor was behind it all along. If you look at the ending, when she said "You", it's because she was shocked to find the doctor in the house, and the realization hit her that he was the one who had been doing the knocking and other things.
Faraday wanted the house, he wanted to live the rich life, and the best way to do it was to get rid of the people who either would object to their marriage or disapprove of them living their if they were married.
He was very manipulative. We saw that in how he would speak to the family members, how he would treat them. "I'm the doctor, I decide who is well," and "You are just tired," and other things. He was a very stiff, morose man, and prone to be domineering. In the end, when he realized he couldn't have Caroline, he decided to kill her.
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