The default setting for the Apple Pencil is to automatically annotate when you use it (Apple Pencil Always Inks). If you would like to scroll with the pencil you can disable apple pencil always inks.
Turn off/ on "Apple Pencil Always Inks":
- From iAnnotate document view, tap the "+" in the top right corner
- Tap the gear icon in the top right corner
- Tap "app settings"
- Tap "annotation"
- Turn "apple pencil always inks" off