iPad Pencil scratching Ipad

What you illustrate is localised surface wear of the anodised finish of the iPad. The illustrated marking appears to correspond with the magnetic contact points of your Apple Pencil. Any abrasive dust or grit that is present when docking the Pencil can abrade the anodised finish of the iPad. 

Basic material science tells us that a hard/abrasive material will embed itself in the surface of the softer material (in this case, the body of the Pencil) - and this abrasive material will 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 - as will lifting instead of sliding) the Pencil from the charging dock.

Based on the images provided, I tend to agree with Lotus Pilot's assessment and advice.

This is purely the result of dirt and grit coming in contact with the outer plastic surface of the Pencil with dirt and grit, some of which could magnetize to the top of the iPad's magnetic surface, causing the abrasions and even embedding some of this harder dirt and grit into the softer plastic material of the Pencil.

The damage you show looks consistent with this being a plausible occurance of materials damages.

This can be minimised by keeping the Pencil's casing clean and free of dirt/grit and any body/finger oils bulid ups and keeping the magnetic side of the iPad clean and free of any dirt and grit build ups.

Oils and acids, from our body's skin, can collect all sorts of stuff that can be transferred and can cause, potential, build up on surfaces that can create areas of of dirt, grime and/or grit that can cause minute scratching and abrasions to materials that make constant contact with each other.

This is not an uncommon thing with many things we use and/or come in constant contact with.

Also, make sure to simply lift the Pencil up and off the chaging magnet without sliding the Pencil off ofthe magnets and being more careful placing the Pencil back down on the magnets rather than sliding to Pencil into place, to minimise any more potential scratching of both device surfaces, from grime, dirt or grit

Best of Luck to You!