When I came to the US for graduate school, the teacher in my electromagnetism course in the first semester (who later became by thesis advisor and friend) was an excellent teacher who wanted us to understand a difficult subject and looked at us for cues as to whether we were following along as he proved various things on the board.
Since I was a conscientious student, I would sit in the first couple of rows in class and would give him what I thought were affirmative head movements to show that I understood. But he seemed increasingly puzzled and once he asked me outright whether I understood or not, despite the fact that I thought I had already indicated that I had.
The problem, of course, was that I was using the ‘Indian headshake’ that is also practiced in Sri Lanka where instead of nodding up and down to indicate ‘yes’, the head has a movement similar to that of a bobblehead doll.
Once I figured out what the problem was, I made a determined effort to replace the shake with a definite nod and over time have stopped using it completely (I think). I later discovered that my friends from Sri Lanka who came to the US also went through similar periods of misunderstanding with Americans before they figured out what was wrong
For those who are not familiar with all the subtle nuances of head and eye movement that originate from the subcontinent, here is an amusing tutorial.