Same thing happened to my '06 Sapphire Black Stingray 5H. On the back by the input jack. The sharpie did the trick as far as coloring the wood.
Now you can consider it a relic. People pay big bucks for Custom Shop Fenders. Like the Jaco Fretless, Fender made a template of the exact ware and tear of his bass.
I hate that to happen to brand new instruments but soon or later you will get more then are you going to patch them up also. It is better off left there. Fender make dings and paint chips on purpose and charge more than shiny one and they call it relic or super relic distressed model and I like them.