Per your update note at the bottom: Yes, people indeed say "I know how you feel," and yet we also say "It's not what you think." I wonder if this is a quirk of English or if it is more universal. At least in English, "it's not what you think" is a self-defense move. It's an attempt to break someone's runaway narrative that is misconstruing facts. Like if I'm scheduled to see you, but I'm stuck at the office a few minutes late and then I get a flat tire driving to you, this might be an "I know how you feel" situation on both sides; but if you are angry at my lateness and accuse me of having detoured to a gambling hall, it's a factually incorrect accusation so I would have to say "It's not what you think" to quickly correct the narrative. If I were to first address your feelings behind the accusation, it would sound as though I were admitting to the fact of gambling. So the phrase may be an attempt to separate facts from feelings and to sort out the facts before we sort out the feelings. Which makes me wonder: What is the "it" in "It's not what you think"? I guess it's factual reality, as in: The real-world facts in this matter do not correspond to your mental representation of them. But also, perhaps, the "it" might refer to normative feelings: What I think you "should" be feeling right now, or what I wish you were feeling right now, is being undermined by your misperception of the facts (especially the facts about me).