It won't be anything to do with Acrobat.
It may well be something with whatever created the PDF, the settings in whatever made the PDF, etc.
Does this happen with every PDF that you do not recreate by printing to PDF (I presume from Acrobat)?
If this is limited to particular PDFs from a particular application and the creator of the PDF is not an Adobe product, what created them?
If it is just some PDFs, can you upload one to dropbox.com and provide a link to it?
Toggle Show Options during the Place and check the options for Crop To.
Thank you Daniel. This worked perfectly.