If at any time your Apple Pencil's battery was depleted, and left in that state over an extended period of time, it will not effectively charge back to 100%. This is true for all lithium rechargeable batteries, not those just used in the Apple Pencil.
If this in not the case and you have recharging this pencil to keep it from being depleted, it just may be possible that the battery is defective ... and, should this be the case, it does come with a one-year limited hardware warranty, and you may find that you can get a replacement for little or no cost to you.