Once in a blue moon, under very rare circumstances, the Tracker may „forget“ to see a file which you know it contains (i.e. you can see that the file is present by viewing the contents of the folder from the Terminal). If this happens to you, close the folder and navigate in the Terminal to a position one directory above the problematic folder. Then type:

rmattr _trk/pinfo_le foldername

Re-open the folder and you’ll be able to see the mystery file.
See also: Check filesystem integrity