Repressed memories are an odd thing. They manifest in our daily lives, in ways we may realize and in ways we may not.
The hallucination Stiles witnessed was just that. A repressed, and maybe even altered, memory. (Lydia’s memory was altered, remember?)
In S2 we are blessed with a heart clenching scene were, high on wolfsbane, Stiles hallucinates his drunken father telling him it was Stiles’ fault Claudia died. Now, this can be one of two things. Another memory (maybe not so repressed) where his father, a severe alcoholic after his mother’s death, spouts things. I don’t know if you’ve been drunk, but when I am I spout random shit. One time I watched a tv show until I passed out and the whole time I was awake, talked about how stupid the show was. Sober, that show is one of my favorites. That’s what happens. Stiles remembers this while high/drunk.
The other option is that it was triggered. Triggers don’t always make sense, sometimes they make total sense. For example, I go into full panic attack, trembling, hard to breath, sobbing, irrational, panic attack when I am around children 2 and under crying. Up until recently, I had no idea why. It stopped me from having my dream job as a preschool teacher. Stiles witnesses his mother blaming him for her dying, a very, VERY traumatic thing for a child, and then she attacks him. It makes sense that this memory would be repressed (dread doctors or not). When dealing with trauma, repression can take place in any age. Children or adults. And when it is triggered you experience pieces of it, not usually the full thing. Stiles, if he was triggered in S2, doesn’t experience the full memory, just the part that really kills him and his mind comes up t with a way for it to visually manifest by showing him an image of his drunk father.
Either scenario, Stiles blames himself. Up until now, we believed that guilt to be irrational. How could a child who sat with his mother everyday she was in the hospital up to her last breath, blame himself for her death. Even as a teen, he knew it was the disease. It was irrational, and even Stiles knew it. And then that little subconscious 10 year old Stiles starts whispering, “She’s dead because of you,” and there is nothing Stiles can do about it, because its subconscious.
Now JD and the writers may just be blowing shit out of their asses, and they don’t make the connection between anything. However, this is for you, as fans, to keep sane, and to make sense of the confusion.