The operating system is informing you that there are still files open by your operating system, and the OS is preventing the unmounting of the volume to avoid data loss. This can be either because there are still files that are meant to be written but are still cached, or that the operating system is using the drive for background processes such as indexing or temporary space. To identify the process that is accessing your disk, you may use Mac OS X's built in utility to identify open files, lsof (click for more information.) Alternatively, you can use third party applications such as What's Keeping Me from HAMSoft  to identify which files are open on your drive.