Instead of saying he's forgotten a plot point or that he's contradicting himself, why don't you try to look at it as him giving Medaka room to grow as a character. Despite all her abilities she's obviously not perfect and will never be perfect. She's partially in denial about something she doesn't want to accept. Get over it.
There's also the point that the word "normal" isn't defined the same way each and every time it's been mentioned in this manga. When someone calls themselves or someone else "normal" you have to look at the context and how they're trying to apply the word.
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