Not enough information. What version of InDesign? How were the original PDFs created, what standard are you using to export and finally, are you sure this isn’t an Acrobat issue?
InDesign 2015.2 downloaded yesterday. I don't know how the original files are created, they are created and given to me by clients. I just know that they print fine in the original PDF. Don't know what you mean by what standard to export. I just set up the new InDesign file by placing several copies of the original PDF on a page and export, that goes to Acrobat DC. I don't know if it is a Acrobat issue, I'm using the current version but I have been having this problem periodically for quite a while now.
Are you choosing a PDF export setting or just winging it and leaving everything at default?