I know that Seat were using older versions of engines than VW, when I test drove cars last at least. So maybe they let the VW brand take the hit on early issues, I dunno..
Still, a 2.0 TDI 140 is the same in a Skoda or a VW, afaik.
Or maybe as you say it’s a factory issue. One of the biggest issues VW had was catastrophic engine failures when just driving along, caused by the oil pump – it was a dodgy design used in one factory, but it was one of the first big issues that started to tarnish the brand image.
I think they still are overall pretty reliable, but they had a few dramatic single issues. The injectors were the other problem on my car – they’d suddenly pack up without warning. Apparently took years of campaigning to get VW to issue a recall.