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Lucy sort of forcibly stops herself from understanding and acknowledging the truth because it would get in the way of what's expected of her. 01 expresses that she wants to keep her around, but it's difficult to justify if Lucy knows their secret and is nosy enough to keep digging. So in order to better fulfill that "perfect" version of herself that's ignorant, she contorts her brain in such a way that she can ignore reality (at least for now).

 

Before the 2.0 update, this wasn't very well-presented or elaborated upon, so in the rewrite I tried to surface these ideas a little better. But ultimately it's a weird quirk of Lucy's personality that might be hard to accept for some, and that's fine.

 

(The out-of-fiction answer is that it's a leftover from when I wanted the series to be more comedy/slice-of-life than drama, and the conceit was that Lucy was too oblivious to recognize a lot of obvious robot tells. If I were to completely start from scratch again, I probably wouldn't end Episode 1 that way, but what's done is done.)