This is fairly common on GTIs I think. My rear discs and pads got changed after not much more than 30,000mi.
The car was occasionally getting put away with damp discs after washing and clearly wasn't getting used hard enough often enough to fully clear off rust that you can get when it sits damp. My rust got to the point where it was wearing the pads excessively. The standard factory ones seems particularly bad for this, so I swapped for a different (mainstream) make when getting them changed.
I now drive the car round the block to dry the brakes after washing I, plus a change of home means that the daily commute is a lot more fun (and warms the brakes up a bit more) too. I've not had any issues since and the new discs always look good.
In short, as suggested above, get some spirited drives in to try to clear off the current marks and if they do, then keep on top of it to save changing your pads and discs ridiculously early!
In 6 months you'll be back wondering about the corrosion on your hubs too!