As the title suggests i noticed the plastic above the rubber seal so whilst tucking it back in noticed rust at the bottom of the seal.  Has anyone this problem?

 

I bought the car 5 months ago as an approved used skoda from Capital Skoda in Newport, dont suppose this would be any kind of warranty fix?

 

 

 

 

Where's it coming from?

The rubber seals have a metal spine inserted within the seal to help the mould and grip the contours of the door aperture. 

 

If the seal is damaged or the spine is exposed then it will rust like that. try cleaning it away and having a good look at the rubber

Well they can't say it's stone chip damage, which is the typical SUK response. If it's a paint issue it's a 3 year warranty, if it's rust coming through a panel 10 year warranty. These seals are known to trap water, and I believe a revised seal is available.