Both worlds are mixing guys. Take it as if our male MC is a virus and the longer he stays on the "real world" it affects more the normal world to be similar to the manwha.
It's so easy to "spread" and to change stuff that even messes up with everyone's minds to replace their personalities to those of the characters of the story he is from. He is confused because he knows the story but not the people. She is confused too because she knows the people but not the story or characters' personality
The world is getting the effects of the story for whatever reason. I think the girls would be in the same situation if our female MC wouldn't have made them realize they don't know the male MC really (but they can't remember the existence of the manwha either) as their minds tries to tell them they do