My 07 plate Mk5 is the same, and on both sides. Had the car from new and its never been damaged. Took it to VW and they said the same as they told you. Not very happy with the service and general response, and the fact I mentioned that if stones have damaged the paint then why does the arch liner drop down further to protect the painted edge that is prone to being damage like the front ones do on the sill (no response, not surprised). I am currently writing to:
Volkswagen UK Limted
Yeomans Drive
Blakelands
Milton Keynes
MK14 5NA
See what they have to say, have brought a 11 plate Bluemotion a few months ago too brand new. Happy with the cars just not the general service, and the fact once a car is brought they are only interested in new customers, not repeat business.
I took the car to another VW garage at the weekend where it was inspected (this time pictures were taken and a case was submitted to head office). This is alot more than the previous VW garage did, as they simply looked at the corrosion and said nope, that's not covered under the warranty.
It turns out that at the top of the arch there is some more corrosion on both sides(this is a common fault apparently).
The guy at VW took pictures of the sill rust and also the rust at the top of the arch.
Word back from VW head office a few days later was that they will replace both arches for the rust at the top of the arch for free, but the sill rust isn't covered under the warranty.
As both arches are being repaired , they are going to need to blend the paint in with each side of the car, they mentioned that for the cost of one hours labor, they are willing to repair the sills as well.
I now need to decide what to do.