This is a known issue with filemaker. You can most easily fix this issue if you use Save a copy... to save a clone of your file and then import the records from your current file into the clone. This process re-indexes your file to correct the problem.
For More Information see: Phantom Record, damaged file message, Recover can't detect a problem
This is one of many acknowledged bugs that can be found in the Known Bug List here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: http://www.4shared.com/file/8orL8apk/FMP_Bugs.html
Thanks! I didn't realize there was such a list. It's a great help.