Please read this:
https://social.msdn.microsoft.com/Forums/sqlserver/en-US/9f9812c3-56cf-4a76-ad48-fad7b03ad9ac/how-to-pass-filename-as-a-dynamic-variable-to-flat-file-source-in-ssis-?forum=sqlintegrationservices
and confirm that you have set the flat file source dynamically.