Acrobat's and Reader's Comment and Drawing Mark Up tools are PDF "annotations". Some of the PDF annotations (such as the Highlight tool) require that there be actual renderable text on the PDF page in order to function.
So, Highlight tool cannot "highlight" if the PDF page content is not renderable text. When might that happen? If you have a PDF with content that is the output of a scanner. All scanners output an image, a picture of the text that was on the paper that was scanned. An image / picture has No Renderable Text. So, nothing to hightlight.
Some other annotations share this requirement.
To resolve this for those PDF files that contain the scanner output simply open the PDF file with Acrobat. Then perform OCR.
Be well...