Perhaps they are PDF files but have the wrong extension somehow. What is the sourse of these files? Were they send by a contact you don't know or who's a little slower on technology than my mother? It's sadly all too common that when you tell someone you need an Illustrator AI file for their logo they just change the extension from .JPG.

So perhaps the OS launches InDesign because the filename ends with INDD. But InDesign parses the content of the file and discovers it's actually a PDF and opens the file in Acrobat. Open it in Notepad. A PDF will begin with "%PDF-1.4" or similar. And Indesign file will be gibberish.