Sounds like the box could well have shat it's pants. Still it's under warranty so only an inconvenience not a disaster.
I love the way people are surprised when cars break. Modern cars are massively complicated and no amount of testing and quality control can completely eliminate failure. You've just been unlucky but at least it happened in the warranty period. Things like this will write off modern cars when they're over 5 years old for people like me. I could afford a 5 year old DSG GTI but I couldn't afford to repair it if the box died.
I wish your GTI a speedy recovery and remember, it could be worse. You could own a MKIII

Nick