Funky Fuel Line or Testy Transmission?

I have a 2006 VW Bug convertible that appears to make a jerking motion when I decelerate and/or brake. I’ve had the car into the dealership and they can’t seem to replicate the problem. I thought it could be a transmission problem, but just read that that year has recorded problems with the fuel system. Could it be causing this problem? Lucky for me it still has 4000 miles under warranty, so I want to get it fixed fast!