Apple pencil 2 keeps getting sort of burn marks

On the basis of what can be seen in your photograph, what you see does not appear to represent burn marks - but something else entirely.

What appears to be evident is marking of the Pencil’s plastic housing by abrasive particles, such as grit - some of which appears to be embedded in the plastic of the Pencil. The environments in which we use our devices can never be totally clean and dust free. Some dust and dirt can contain hard mineral materials, that can cause cosmetic surface damage where the material can become trapped between surfaces (for example, where a magnet may attach the Pencil to the corresponding surface of the iPad).

Material science indicates that hard materials will embed in softer materials. This would perhaps appear to case with your Pencil; dirt and grit from your environment has become embedded in the soft white material of the Pencil body at its magnetic contact points with the iPad.

As for the possibility of burning, you might be able to reasonably discount this a viable hypotheses. The inductive electronic components, that transfer charge between the iPad and Pencil, are located in the region between the two magnetic contact points. Any visible evidence of localised heating, caused by inductive charging, would be observed between the two areas of surface marking of your Pencil.

If you have any concerns, you should take both your iPad and Pencil along to the Genius Bar at your local Apple Store - where the technicians will be able to test and assess your devices.

The marks will line up to the magnets on the case or device.