"File and Content" report is a great feature, but unfortunately not as powerfull as it should.
Currently, the report has been designed to display only part of the files you have access to :https://help.salesforce.com/apex/HTViewSolution?urlname=Why-a-file-does-not-appear-on-the-File-and-content-report&language=en_US
If a file is shared privately through a record Chatter feed and that you have access to this record, you'll gain access to file. However, the file won't be visible in the report. It needs to be shared to you directly, even with just viewer rights, to see it on the File and Content reports.
This makes no sense, we should have the same visibility access on the report than on the file itself.