In Practice Questions Mode, you will not see a duplicate question until you have exhausted every question in a particular subject area.
In Practice Exams Mode, you are presented with questions based off your selections and not necessarily your areas of strength or weakness, so it is quite possible that you'll see a duplicate question within this mode.
Please note that questions will begin to repeat even if you have not exhausted them all if you have selected "Exclude OPE Questions". Selecting this box reserves these 400 questions to take as practice exams as the MBE approaches, ensuring that you have not seen them during your studying. It is possible that the only questions you haven't seen belong to an Online Practice Exam. If you are not planning to take the OPEs, de-select the box beside "Exclude OPEs" and continue to answer questions in Questions Mode.