Headliner was wet where the driver's side A-pillar met the headliner, and water dripped behind the dashboard into where quite a few expensive electronics are. Was getting quite bad, so I removed the headliner and watched where the water was coming from during a rainstorm. Was coming from where the sunroof assembly met with the roof. This is due to poor quality sealant from the factory. The proper way to fix this is to drop the assembly and apply good quality caulking.

The sun roof leak into the roof liner creating a nice stain near the passenger roof handles. Contacted Volkswagen about it and they said that its not a warranty issue. They listed it as a technical issue so that they didn't have to issue a recall. Nice job Volkswagen.