User blog comment:FairyRaven/Fairy Tail Chapter 329: Seven Dragons, Review and Commentary/@comment-7505640-20130501071155/@comment-7418318-20130501083914

Theoretically Cobra might have gotten that scar when Nirvana collapsed, since we never saw him again after Brain shot him in the back.

But I too think that the KotSS arc did happen in the manga too and the scar comes from sacrificing his eyesight in exchange for power.