Water leak in the tailgate

Hey guys. I need some help, and I hope somebody else have some experience with the same problem.

I just came back from abroad, and open the trunk, after 2 weeks. Car was parking and it was raining a lot here, as I heard. I opened the trunk, suddenly water poured in to the boot from the tailgate, through the plastic trims on the tailgate. 

I had previously some dropping in the same way in to the boot, since I bought the car used (only 3,5 years old) but I thought it's some condensation. 

I took the car to the Skoda service today, and they said that the rear wiper and between the glass there was some gummy ring that was leaking. 

Plus they removed 3 bungs(gummy rings) from the holes on the bottom of the tailgate l, so the water can come out. I do not think it should be removed (rust problems later on) but they did it anyway. I would like to ask somebody to take a picture of those bungs from outside (if you have a stationcar/wagon).

Does anybody else had problems with the tailgate? The want me to pay around 100£ even though I told them, that I had this problem several months, but the water amount yesterday was crazy lot and I call them right away. The used car warranty is gone like a month ago, so they want me to pay of course.

Thanks in advance for any kind of info