Although it’s immensely popular, repairing permissions is a waste of time unless you have a specific indication of a permission error involving system files, which is rare, or a boot failure. It is not a universal rite of healing for computers. It has traditionally spewed bogus warning messages that mean absolutely nothing.
The built-in help for Disk Utility reads in part:
If you see an alert or a message that says your permissions are set incorrectly, you can correct the disk’s permissions by clicking Repair Disk Permissions.
It’s justifiable, though rarely necessary, to repair permissions after running a third-party software installer, as defective installers have been known to damage the permissions of system files.