@Michele – if placing PDFs you have import options in the dialog of selecting a PDF file.
Tell InDesign to "crop" these PDFs to "Media". That should work.
More information about the "boxes" in PDFs here:
Or use the search engine of your choice to find even more on this topic.
@Michelle – that is bad…
What you can try:
Go to your Adobe Acrobat Pro software (not Adobe Reader!), open one of the PDFs you cannot place, and save it:
A. With a new name, then try again to place that.
B. Save it as EPS, then try to place that EPS.
If that will not work, I need a sample of one of your PDFs – send me a personal message, so that we can exchange email addresses – so that I can try something in Acrobat Pro's Preflight panel to get this straight.