InDesign is great and versatile but sometimes there are issues which make one scratch the head for quite some time and afterwards come up with a working solution.
Recently I've started another book project and after placing word files I discovered, that some special characters were missing, soft hyphens, for instance were not imported into InDesign.
But as it turns out, it is not InDesign causing this, it's Word and its file formats.
InDesign - Hyphens missing - solution
Text materials received were in docx format. Opening and saving them from docx to the good old doc seems to have solved my and our troubles. If files are in doc format, try saving them as docx and give it another try by placing these files into InDesign.