The Node Access system in Drupal provides a powerful way to provide granular access to individual nodes, but it can occasionally cause unexpected problems.
Consider a case I ran into the other day: I had a View that was supposed to show all files managed by Drupal, however some users could only see a subset of the files. My initial detective work took me the wrong direction (I was using the File Entity module and spent a little time investigating its file access system) but eventually I realized that:
Do you have a View that's not showing all the results you expect? Perhaps Drupal's node access system is interfering with one of your relationships.