I would guess that the paint has been chipped off by something being put in the car and that the seal has trapped water there which has caused the corrosion, MK3's don't go rusty if looked after, they are too well made for that, Best bet is to get it sorted out now before it gets too late, also seeing as its inside the door jamb it should be fairly cheap as you shouldn't need to blow the colour in too match to original paint down the side of the car.
The MK2 had a problem if you remember on the little rubber boots that carry the wires into the tailgate, rust would form around the boot and eventually the boot wouldn't have any metal to hold too. the little gromets and boots on cars are terrible water traps and it might be a good idea to go round the car with waxoyl or similar just to give them a coating to prevent rust.