Translation:I do not completely understand the question.
wording order can sometimes be very important in VNmese.
in "tôi không hoàn toàn hiểu câu hỏi," không is modifying "hoàn toàn hiểu" (totally understand). it means I do not understand all the question, just partially.
in "tôi hoàn toàn không hiểu câu hỏi," hoàn toàn is modifying "không hiểu" (not understand). it then means I do not understand the question at all.