There is another possibility that has not yet been mentioned in this thread. This may be your problem.
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.
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.).
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. Place the resultant PDF file into InDesign and missing content due to annotations will appear. (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!)
Let us know if this resolves your problem.
- Dov