Try going to Settings/general/accessibility/zoom and turning off all zoom settings
If you use zoom settings a lot this is still a problem, even though turning zoom off solves the apple pencil problems.
Until Apple fixes the problem, I suggest turning on the accessibility shortcut feature.
1. Go to Settings/general/accessibility/Accessibility Shortcut
2. Check the Zoom feature
Then, when you want to turn zoom on from within other apps or from the home screen, just triple click the home button. Now, the zoom feature stays on. So, if you triple tap the screen, it zooms in and out like before. And, if you go back to settings, you will see that the zoom feature is turned on. Because of this, your apple pencil will begin to have problems again. However, if you want to turn the feature off while using the pencil, you can quickly do so by triple tapping the home button again. So, if you use the pencil a lot, leave the zoom off and triple tap the home button when you need it. On the other hand, if you use the zoom a lot and the pencil only occasionally, leave the zoom feature on, and triple tap home to temporarily shut it off only when you want to use the pencil.