Why does Winston think he "killed" his mother in the book 1984?
The key words are: indoctrination and manipulation. Indoctrination and manipulation, as every reader of 1984 knows, are the key strategies of the Party to maintain control of the population.
This manipulation is evident in the story of Winston. Main character Winston has an issue regarding his memory and the possibility that he was responsible for the death of his mother. This doubt, and its eventual realization, occur in chapter 7, book 2 of the novel. As readers, we are led to consider that he is more than likely not guilty at all of her death, but the system needs for him to second guess himself so that guilt and weakness can take over him. In the Party, power is about dividing and weakening the citizen.
Yet, in chapter 7 we find that Winston may be shifting his thoughts regarding his mother, when he tells Julia that he "had thought until then" that he was guilty.
until this moment I believed I had murdered my mother...
Notice that this chapter gives us insight as to the inner thoughts of society under the control of the Party versus the independent and individual thoughts and emotions that Winston is starting to foster through dreams and memories.
Like the prole, he has the ability to establish emotional attachments and, deep inside, he knows that he wants to establish them openly.
All this being said, the easy answer to the question as to why Winston thinks that he killed his mother is because he is falsely associating two separate events, one involving a theft of chocolate, and the eventual killing of his mother and his sister, as sequential events.
The fact is that the taking and killing of his mother and sister had nothing to do with Winston. However, the Party needs for him to continue to be confused, guilty, and feeling weak, in order to maintain the control of Winston and everyone who dares question the "order" of things.