Hi - I had the same prob.
The CC has double door seals to provide a silent driving experience.
Mine was a late 08 build so reasonably early in the model's life.
Water would accumulate in the door sills (3 out of 4) after rain or hosing the car and almost fall on your feet when you opened the door. It sits there and simply doesn't drain - posing a rust risk and if there's enough water in theory it could spill into the cabin (which it did once).
Much harassment of VW dealers led to discussion with Germany and a set of replacement seals were designed, made, and despatched.
VW had my car for 6 weeks (they provided a loan CC with similar config so I didnt care too much) and the sills were sanded back and repainted as rust was showing already after only 6 months of ownership and the new sills installed.
All under warranty and no charge.
Car is fine now.
I've heard stories from other CC owners being told by dealers it 'didn't matter' or 'was normal' - I suspect with all the cars VW have to deal with we can't expect them to know every quirk of every car and it was a new model at the time - but your problem needs to be addressed soon to avoid serious rust which may not initially be visible.
Chatswood Classic looked after mine so if no luck in your neck of the woods get in touch with them and ask them to instruct your dealer what to do.
Cheers!
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