I discovered the same problem and found an easy workaround, but it can take quite long when you have a lot of pages in the PDF-document that you plan to annotate. I opened the document with the built-in preview app and exported a page as .jpeg-file (other picture formats might also work - haven't checked them yet). Then import the .jpeg file into your Evernote. The annotation feature for the .jpeg-file worked without any problems on my MacBook Air with Sierra installed. Maybe someone has an idea on making the .jpeg-exporting-process a little less time-taking? Via the preview-app I can only export one page at a time.