What you describe is localised surface wear of the anodised finish of the iPad. The marking will 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 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 - this being a gradual process over time. Keeping these surfaces clean and dust free can reduce the possibility of cosmetic surface damage.
Any marking is purely cosmetic - and has absolutely no relationship or relevance to the functioning (or not) of your Pencil.
These support pages may be helpful with pairing and use of the Pencil with your iPad:
Connect Apple Pencil with your iPad - Apple Support
Charge your Apple Pencil and check the battery - Apple Support
Be aware that if your Pencil has been set-aside for an extended period, unused and uncharged, the Pencil battery may have been damaged through deep discharge. In common with all Li-ion batteries, they must always have some level of charge.
The tiny internal Li-ion battery is susceptible to permanent/irreversible damage through being left discharged for long periods. Even some “new” pencils can exhibit signs of failure out-of-the-box if they are “old stock”.
It is essential that if you have an Apple Pencil that you charge it regularly - whether used or not - so as to protect the battery from deep-discharge. Do not allow a pencil to remain in low-charge state for any period of time - as the internal battery will fail, rendering the Pencil useless. Setting aside an unused Pencil, for extended periods, is a recipe for premature death of the Pencil battery.
If the Pencil Battery has failed, the only remedy is to replace the Pencil. If the battery has failed and your pencil is within its one-year warranty, you should look to having it replaced by your retailer or at an Apple Store.
Gentle warming of the Pencil (such as placing on a hot water radiator), prior to attempting charging of the Pencil, can sometimes resurrect a dead Pencil battery.
