Hope you are doing well. I am sorry to hear that you are unable to scroll down the PDF when you are annotation mode.
However, this is how the application is designed to work.I would suggest you to remove the selection of the pencil when you have a requirement to scroll down because, if the selection is at a pencil, the application by default thinks that you want to write and not scroll through.
Let me know if this helps.
Thank you for contacting us. In order to scroll pages in Commenting mode while using Apple pencil/stylus, please use 2-finger to scroll pages instead.
Hope this help,