Hello S Norton,
Thanks for reaching out to us with this question about using OneNote on your Surface Pro 3. I'll do what I can to help you.
Thanks for the feedback on this issue. I was able to reproduce the issue you describe here on my Surface Pro 3. I understand your frustration with this. I found that if you use the modern version of OneNote, these problems do not occur. That version does not move up and down when these buttons are pressed. Another workaround you could use is briefly disconnecting the cover when you are going to be writing or drawing a lot by hand, but I understand if that is an undesirable workaround.
Please let us know if this helps and if you have any further information for us.
Best Wishes,
Zack_T