Today I discovered that upon converting a Word file into a PDF (either via "Print" or Save As > PDF), Word automatically modifies Figure, Table, Equation etc. references that I've inserted via Insert > Cross-reference. It makes them into reviewer comments, changing their colour, underlining, and requiring the user to "Accept Change". It also inserts full equations in-line by their reference and bold-faces references, whereas I previously turned that feature off. The error occurs despite "Track Changes" being "off" and persisted on a PC. The Internet suggested this has something to do with hidden bookmarks, although I did not find any remedies to the problem (although others seem to be having the issue as well e.g., here).
Unfortunately the only solution I arrived at was to re-type all references where they were previously inserted via cross-reference. Even then, some elements of equations appeared as reviewer comments (e.g., only the division line in an equation appeared as a comment, while the rest of the equation stayed normal; strange!). In order for these not to appear red (as comments) on the PDF, I needed to change the document vew to "final" rather than "final showing mark-up" in the Review pane (image below). Accepting each change does not solve the issues, as they automatically become comments again upon converting to PDF.
Unfortunately the only solution I arrived at was to re-type all references where they were previously inserted via cross-reference. Even then, some elements of equations appeared as reviewer comments (e.g., only the division line in an equation appeared as a comment, while the rest of the equation stayed normal; strange!). In order for these not to appear red (as comments) on the PDF, I needed to change the document vew to "final" rather than "final showing mark-up" in the Review pane (image below). Accepting each change does not solve the issues, as they automatically become comments again upon converting to PDF.
I'm using Microsoft Word for Mac 2011, although I believe this issue exists in other versions of the software. This experience as well as others reinforces my prefer for LaTeX over Word. I generally use LaTeX for everything, even class notes, but could not use in this instance per the requirements of an academic journal.