That having been said, the fact is that the only way to find out is to open the PDF file in Acrobat Pro DC and ascertain exactly what the non-printing items are.
(2) You are correct only in that I don't know exactly whether the OP's problem has to do with annotations in the original PDF file although in the vast majority of cases with these symptoms, that is exactly what the problem is. (And quite frankly, I don't think you know anything about me and my role at Adobe over the last nearly 30 years! Stop guessing! And this is not a joke!) I have nothing to “envy” one way or the other. (1) FYI, most of my work is done on Windows-based systems although I also have and use a MacOS-based system as well.
Let us know if this resolves your problem. (Note that when this fixup is applied in Acrobat, the content that was previously editable as annotations and forms will no longer be editable as such!) Place the resultant PDF file into InDesign and missing content due to annotations will appear. To get such PDF content to not be ignored, you must open the PDF file in Acrobat Pro DC (or Acrobat Pro 2017), invoke Acrobat Preflight, choose the Acrobat Pro DC 2015 Profiles and from the PDF Fixups group, select Flatten annotations and forms fields and press Analyze and fix, storing the resultant PDF file as a new PDF file. This other content includes any form of annotation including but not limited to forms fields (including protected forms fields that appear to be standard PDF text), stamps, signatures, watermarks, and review markings (highlights, underscores, crossouts, underscores, insertion points, text boxes, arrows, lines, polygons, scribbles, etc.). When you place a PDF file into an InDesign document, only the “base PDF content” is placed “other content” of the PDF file is ignored.
There is another possibility that has not yet been mentioned in this thread.
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