Though many issues with your Mac may indeed only require a simple trip to Disk Utility's repair permissions function, sometimes users find that a list of permissions are found to need repairing and never do. In a recently updated article, Apple outlines many of these permissions messages that you can safely ignore.
Disk Utility, when verifying and/or repairing permissions, will check to make sure objects installed from package files maintain an updated "Bill of Materials" (a .bom file). When there are differences between what the system is and what it should be, Disk Utility reports the difference in the error log.
From an Apple knowledge base article:
Many things you install in Mac OS X are installed from package files (whose filename extension is ".pkg"). Each time something is installed from a package file, a "Bill of Materials" file (whose filename extension is ".bom") is stored in the package's receipt file, which is kept in /Library/Receipts/ . If you look in the Receipts folder, for example, you should see all kinds of files that end with .pkg, including some that were created when Mac OS X was installed (for example, BaseSystem.pkg). Don't worry, these files don't take up much disk space and you shouldn't put them in the Trash.
If you are getting a list of permissions errors that cannot be repaired (or continue to show up in your error log window), check them against this list from Apple.