We get PDF's from all over, often they are made up obviously using greyscale images, along with spot color, but at some point file gets changed to color, so that when placed in Indesign, they won't separate to black w/spot color. Is there anything that can be done at this point, or must we always get back to advertiser to straighten it out. Most often we don't know what software used, or their skill level. (or ours...!)
If you are having an issue in InDesign, why post here unless you are editing the PDFs, which you shouldn't have to as long as they are correct.
If I have an issue with an advertiser's PDF, the first thing I do is open it in Acrobat and make sure it is as per submission guidelines. The only other problem once in InDesign is if there is a profile to profile conversion occurring at import or output.
As well, in either Acrobat or Reader, you can look at the document properties. Unless the PDF is produced via postscript and distilling, what it was made in should be listed.