I can't speak for the warranty, but some stainless steels will rust, like low chromium stainless steels that OEM's use (304). Also galvanic corrosion will occur when dissimlar metals come into contact with each other, and in the case of your flange, there's a high probability that the material the flange on your Borla is a different grade to the flange on your y-pipe. Also the fact that the flanges are heated, accelerates the corrosions process.
