alt Hacker NewsI don't think this is helpful if somebody is trying to learn English subtleties. Responding to a person's thought with "You don't understand", and that's it, implies hostility/rudeness.
People tend to read certain things with a negative tone because people tend to write certain things with a negative tone. That kind of pattern recognition is fundamental to language, not a regrettable quirk. Otherwise "You have absolutely no idea what you're talking about" would be equivalent to "I think you might have misunderstood".
I had to double check to make sure I responded to the right person after seeing this pop up in my replies summary :D. One way to perk up during morning coffee!
I'm sorry you feel "you didn't understand" has a similar range of interpretation as something like "you have absolutely no idea what you're talking about". I'm not sure I can help with that, I can only say this is not the interpretation of every native English speaker. If anything, the split in views should hopefully help convey English often cares about context and the audience over a singular meaning for a set of words (though I don't think that's particularly unique to English).