Maybe you can try and run the Accessibility Checker in Microsoft Word before exporting to PDF.
The Accessibility Checker wizard will identify issues and provide you with a list of options to fix.
After you apply the fixes, save the file and then perform the export.
It is also important to watch for the file conversion method that you may be employing.
Save As, Print to pdf, or export to PDF directly from Microsoft Word (specifically using the Acrobat PDFMaker COM Add-in) will and may render different PDF output results.
In which case you may want to test with all methods and compare which one produces the best PDF structure.
From what you've described, it seems like if it could be an issue with a character set that is not properly mapped due to half-space Unicode fonts such as math symbols (just a guess in the blind here), or simply an text encoding issue.
Using the Accessibility Checker may help you with that and also employing the Compatibility Checker.
See if this old Microsoft Support guidance is relevant: