During my seminar when my teacher asked a question, rather than saying that "I am not able to understand what you are asking", I said
"I don't know what you are saying"
due to anxiety of being on stage. Was I totally offensive?
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Being offensive is not only with the choice of words, but with the tone of voice, facial expression, gestures and other body language. However, you were not being polite in that scenario, where I presume from the question your teacher was definitely offended. I cannot blame you totally because you said that you were too anxious, and you chose rather the wrong set of words.
"I don't know what you are saying" in itself is not offensive. There are no offensive words or offensive impressions there. If you were saying that to your friend, it would be normal.