OK, I know this topic has been done to death, but I had an unusual one. The leak was from the rubber seal at the front corners or the roof. The seal had come away from the sealing edge and needed to be re-stuck with double sided tape.
We had three days of continuous torrential downpour last week (after two months of bushfires) here in the Blue Mountains of Australia. We had 0ver 400mm in 3 days which was almost the total rainfall for the whole of 2019. The panoramic room gutter drains couldn't keep up with the flow so the gutter filled up and leaked into the roof liner, and into the front footwells.
Also, Skoda has also put some nice square holes just ahead of the rubber seal so if the gutter does fill up, it will drain through the square holes into your roof lining. Thank you Skoda. I placed some tape over the 5 square holes, ready for next time....