In Practice Questions Mode, the program is designed to not show you a duplicate question until you have exhausted every question in a particular subject area.
In Practice Exams Mode, you are presented with questions based on 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 the "Exclude OPE Questions" or "Exclude MBE Study Aid Questions" option.
Selecting either of these boxes reserves the 600 questions in these exams for you to 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 or MBE Study Aid if you have either of these being excluded in Practice Questions.
If you are not planning to take the OPEs, de-select the box beside "Exclude OPE Questions/Exclude MBE Study Aid Questions" and continue to answer questions in Questions Mode.