Hi,
I had the same issue with the rear door leaking in water after heavy rain a few months back. I had to remove rear door card, undo the bottom of the 'inner' door card (few bolts), dry it out, then apply lots of 'plumber golds' sealant (translucent), fasten back up the bottom of the inner door card and leave for 24 - 48 hours to set. Re-tested, no more leaks. Basically the rubber inner door card seal had failed, poor really on a 5/ 6 year old car. Re-assembled the door, all looks normal. I did look into replacing the inner door card, but it is riveted on in places, and is around £100 from TPS as it comes complete with electric window motor etc.
Very common on skoda fabia's, take a look on youtube for videos.
Hope this helps, good luck!