A few years ago I bought an Octavia MK1, to find out a few days later that there was water ingress showing in the rear passenger footwell, left-hand side.
Its origin: the rear left door. At some point the window elevator was replaced and not only the plastic film was missing, but a bubble wrap green plastic had been left inside the door for no apparent reason (with the skoda logo and all), directing water to where it shouldn't be.
I cleaned the inside of the door, bought an original plastic film, used an hair dryer to get rid of all the moist and it has been fine for around 5 years.
The rest of the doors were also inspected later, only to find out that all the protective films were missing or damaged, probably because these cars are prone to window elevator malfunctions.
I replaced the foam films in both front doors (16€ each), and the plastic film in the remaining rear door (7€).
Part numbers for the protective films (In Portugal, LHD):
1U4 868 395 F - protective foil for front left door
1U4 868 396 F - protective foil for front right door
1U4 868 399 - protective foil for rear left door
1U4 868 400 - protective foil for rear right door
@Funkoid If the plastic film in the boot lid is not there doing its job, it may be the culprit for the water ingress. I have also tried to buy that one, but it was discontinued by Skoda.
Part number:
1U9 867 141 - boot lid protective film