I have a brand new iPad Pro. I have this problem with the Apple pencil as well as the iPad itself. All cables, adapters, etc. are Apple products. I haven’t noticed that the charging stops at any particular percentage, but I’ll keep a lookout for it. If anyone comes up with a solution, I’m listening. (Apple Store is at least two hours away.)
Edit: I suspect a poor fit inside the lightning port, where the device meets with the cable/pencil.