She's aware. She just thinks that by denying, you will beleive her and think that no such conversation ever takes place.
The storage and retrieval error goes like this: if you say something innocent or with more than one possible meaning, a woman will choose the worse possible meaning and store the feeling of her emotional reaction to it, without storing the circumstances. Then, when the issue comes up later, she will play back the stored feeling and the discussion will focus on what you must have said to make her feel that way regardless of what you actually said originally.
And she will be completely unaware of the process and if you point it out, well, she knows what you must have said or she wouldn't have felt that way. You will lose this conflict, bank on it.