The Disk Utility app in OS X 10.11 has been significantly overhauled, and one major change is the “Verify Disk Permissions” and “Repair Disk Permissions” options have been removed. Historically repairing the permissions has become a routine OS X troubleshooting technique.
This change is due to El Capitan’s new System Integrity Protection (SIP), a.k.a. rootless, which restricts root-level access to protected system files. SIP also automatically ensures permissions are set according to the developer intensions when OS updates are applied, therefore repairing the permissions should no longer be necessary.
Also of note, in the verifyPermissions options repairPermissions options have been removed from the command line diskutil with OS X 10.11.