We seldom meet this problem, so sorry! Maybe it's because the Mac is not under the latest system and the pdf had left blank before in iPad.
I have this. It’s a problem with the pdf rather than marginnote. Often easily fixable on the iPad by recreating the pdf, (possibly with the desktop, too, but I use ipad more).
- Open pdf on ipad
- Go to print
- Swipe fingers open on the print preview of the document to open it as full size preview
- Save document as new file.
Often this works. In this screenshot, the yellow highlight is the odd behaviour before. The highlight doesn’t cover all the text. The grey highlights after after - now in line with the text. You can see this is not in marginnote (this is the highlights app) but then send it back to marginnote and that, too, highlights as expected.