InDesign is great and versatile but sometimes there are issues which make one scratch the head for some time and afterwards come up with a working solution.
Recently I've started another book project and placing files from word it was discovered, that some special characters are 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.