My 5 door Gti had exactly the same problem - but all along the trim strip. The insides of this strip are metal, and can rust over time causing the trim strip to bulge at various places - not very neat looking! I tried various scrappys and couldn'd find a decent condition one. Ended up going to VW (spat on their floor as I walked in) and payed for a brand new one: about ?22 I think. At least it looks OK now.
According to a VW specialist I spoke to these trim strips are well known for doing this, and having looked at other Gti's it does seem quite common.