I repair my permissions regularly via the Terminal.app and there is always some stuff that went askew. No biggie. The real determining factor is if your Mac is exhibiting any wonky behavior. Permissions have to be WAY out of whack for that to happen.
I usually run the repair command several times in a row. A second pass often picks up things that were missed in the first pass. If you want to run it from the Terminal.app, copy/paste the following into a Terminal shell (window) and hit Enter:
diskutil repairPermissions /
The spacing and capitalization are critical which is why I recommend copy/paste.