Many users of Apple Pencil often misidentify cosmetic marks, that appear on their second generation Apple Pencil, as burn marks.
The marks usually correspond with the magnetic contact points of the Apple Pencil to the iPad - and are due to dust or grit (common in many environments) present when docking the Pencil the iPad. Corresponding marks are sometimes seen on the iPad itself. These marks are cosmetic - and do not affect function of the Pencil or associated iPad.
Basic material science tells us that an hard/abrasive material will embed itself in the surface of the softer material (in this case, the body of the Pencil) - and this can abrade the surface of the harder material (the anodised coating) as the Pencil slides on/off of the iPad charging pad.
Keeping these surfaces clean and dust free can reduce the possibility of cosmetic surface damage.