Newbie here and all, but I just noticed the same on my 1-month-old GTI and I can't figure out why people are not concerned about this.
I understand that water needs to be able to pass through the door and that the door is designed to withstand this penetration with a wax coating. But this is a different issue altogether. Standing water in the door is a different beast than water that can easily vent from the car and it concerns me for three reasons: 1. ice formation, 2. increased likelihood to rust in marine environments like mine and 3. mildew/mold growth in the summer (small hot and wet environment).
The point can be made that if you drive your GTI every day then the rust and mold concerns go away because the water drains on a daily basis, but in colder climates, ice is still an issue and what if I don't drive my GTI for 2 weeks if I'm away?
I took it to the dealer and they said they 'fixed' it without giving me any confidence whatsoever. They didn't say it was normal at all. My gut reaction is that I just bought a car with a design flaw that needs to be fixed. If there's a design reason behind this experience I've love to know why it is designed this way, but so far no one can point to specifics, they just say 'it's normal.' I would like to understand why I should not be concerned about ice, rust and mold and would love any insight into what's causing the issue.