What could change the disk permissions?

When I talked to an advisor from Apple Care, he asked me to do "verify disk permissions" under the First Aid tab of the Disk Utility software. These are the various read/write/execute permissions of Unix file systems. To my surprise, there were about 7-8 files' permissoins were changed.
What could change the file permissions? Some of the files are related to Safari which I don't use at all.
The reason I contacted Apple Care is that my Mac Pro lost the sound output after I woke it up from the sleep mode. There was no sound output from iTunes or YouTube vidoes. That is why I contacted AppleCare. After I did a "repair disk permissions", the sound output returns.

You are looking at the report by Disk Utility as it repaired permissions on files based on the permissions database of your OS X installation. If those permissions differ from the file's actual settings, then Disk Utility changes them to conform with the database's permissions.
In most cases the reported information you see in Disk Utility are false positives that result in no real change but just an information message that you can ignore.
In your case it's probable that one of the apps you had open made an improper write to the disk when you put the computer to sleep, and that ended up changing some file permissions that should not have been changed.

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