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Do you have any pictures?

If it's stainless then it's possibly an area of pitting which is holding onto the carbon deposits making it very hard to clean and may give the appearance of flaking chrome in concentrated areas. This is mostly found on the lower curve of the pipe as that's where excess fuel/water makes the most contact. A good going over with some 000 wire wool and a mild metal polish followed up with high temp metal sealant would sort it out. This is basically what I had to do on the stock 335i pipes which weren't plated. But that was a '56' plate so might be totally different to D's and/or later models.

If it's chrome plated then I'm not sure if your warranty would cover it as depending on how it's been worded it will most likely only cover the mechanical integrity of the exhaust system and not the cosmetics unless of course they are removable tips, in which case there's a good chance you can get them replaced.

In any case it's worth chasing. Don't ask, don't get.