Closing Sprint caused some issues to go to Not Applicable

[chris.reyes]

I had a sprint that crossed multiple projects with some issues that were left in To Do state.  When  the sprint was closed, the issues went to "Not Applicable" for a particular project.  At first, I thought it was just issues that had sub-tasks assigned and were marked as done.  But now I'm being told that they were not.  Any idea what could cause this and how I can make it so that in the future when I close a sprint it doesn't move those issues to Not Applicable.  Thank you.