Are you certain that it was present when removed from the box, before use, or did you notice this after the Pencil had been paired and used for the first time?
As described, you might have a very tiny cosmetic blemish. If you cannot feel the blemish, it is unlikely to offer any threat to the cosmetic finish of your iPad. You should however, be sure to keep the mating surfaces clean of dust or grit when docking the Pencil with the iPad to pair and charge. Environmental dust and dirt can be abrasive - and, over time abrade the anodised finish of the iPad chassis.
If purchased directly from Apple, if you are unhappy in any way, you have benefit of Apple’s very generous 14-day returns period - within which you can unconditionally return an Apple product for exchange or return.