Hybrid case?
Your Apple Pencil Pro can optimally charge only when physically docked with your iPad's inductive charging dock. Anything between the Pencil and the iPad will interfere with, or reduce, charging performance.
If you continue to experience difficulties, you might be advised to visit the Genius Bar at your local Apple Store or Apple Authorised Service Provider (AASP) - where the technicians will be able to test and assess your iPad and Pencil:
Genius Bar Reservation and Apple Support Options - Apple
If the Pencil was purchased directly from Apple, in many countries you have 14-days within which to unconditionally return the Pencil for exchange or refund.
Be aware that unless the Apple Pencil remains totally motionless, its Bluetooth radio and electronics will remain active - and will deplete the Pencil’s tiny battery just as quickly as when it is being actively used with the iPad. As such, a Pencil that is not docked with the iPad - such as being carried in a case or pocket (even intermittently) - will appear to lose battery charge while it is not being used.
By contrast, if the Pencil is set aside and it remains motionless, the Pencil will shut-off - and will retain its charge for many days/weeks.